Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	178	959	T→C	intergenic (–/–)	– / –	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	178	959	0	T	C	97.9%	156.8 / ‑4.8	48	intergenic (–/–)	–/–	–/–
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (19/28);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 4.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GGTAAGATTTAACATATCCGGGGATTTGAAGCCGATAAATCCTGATAAATATCCATGAACGTAAAAATCAGATACAGCCTGTCGGCCGCTGTTCTGGCACTGATTGCCGCCAGTGCTCCTGCCCCTGACATTCTCGATCAGTTTCTGGATGAAAAAGAG  >  178/898‑1056                                                              |                                                                                                  gggacagataaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACt                                                            >  2:674865/11‑101 (MQ=255)  ggacagctaaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCGATGAACGCAAAAACAGGATACGACCTGCCGGCTGCGgtactggtactg                                                           >  2:1631107/10‑101 (MQ=255)  ggacagataaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTg                                                           <  2:659166/92‑1 (MQ=255)    acagataaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGAt                                                         >  1:1197181/8‑101 (MQ=255)     cagataaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGAtt                                                        <  2:1396358/95‑1 (MQ=255)      agataaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTg                                                       >  2:4284/6‑101 (MQ=255)      agataaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTg                                                       <  1:1027431/96‑1 (MQ=255)      agataaaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTg                                                       >  2:154656/6‑101 (MQ=255)        tttAACATATCCGGGGATTTGAAGCCGATAAATCCTGATAAATATCCATGAACGTAAAAATCAGATACAGCCTGTCGGCCGCTGTTCTGGCACTGATTgcc                                                     >  1:1586216/1‑101 (MQ=255)           aaCATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTgccgtc                                                  <  2:672952/101‑3 (MQ=255)             cATATCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTgccgtcgg                                                >  2:1411185/1‑97 (MQ=255)              atatCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTgccgtcggt                                               <  1:1558566/101‑6 (MQ=255)              atatCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGGCGGCTGCCGTTCTGGCACTGATTgccgtcggt                                               <  2:1163612/101‑6 (MQ=255)               tatCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTg                                              <  2:1313376/101‑1 (MQ=255)               tatCCAGGGTTCAGAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTg                                              <  2:1074918/101‑1 (MQ=255)                   cagggttcagAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGcc                                          >  1:1122916/10‑101 (MQ=255)                    agggttcagAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCt                                         <  2:973764/93‑1 (MQ=255)                    agggttcagAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCt                                         >  1:630300/9‑101 (MQ=255)                    agggttcagAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCt                                         >  2:124465/9‑101 (MQ=255)                    agggttcagAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCt                                         >  1:754578/9‑101 (MQ=255)                      ggttcagAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGc                                       >  2:241240/7‑101 (MQ=255)                          cagAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTgcgcctgcgcct                                   >  2:152024/3‑101 (MQ=255)                          aagAACCCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTgcgcctgcgcct                                   <  2:322058/99‑1 (MQ=255)                           agAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGcgcctgcgcctg                                  >  2:1449259/2‑101 (MQ=255)                           agAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGcgcctgcgcctg                                  >  2:773086/2‑101 (MQ=255)                            gAAACCGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGa                                 <  2:402908/101‑1 (MQ=255)                             aaaccGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGat                                <  2:280837/98‑2 (MQ=255)                               accGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGatat                              <  1:224897/100‑1 (MQ=255)                                 cGATAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATtc                            <  2:1409888/101‑1 (MQ=255)                                    tAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCg                         >  2:1463263/1‑101 (MQ=255)                                    tAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCg                         <  2:1012972/101‑1 (MQ=255)                                    tAAATCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCg                         <  1:588304/101‑1 (MQ=255)                                       aTCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGacc                      >  1:1344063/1‑99 (MQ=255)                                       aTCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGacc                      >  1:1251641/1‑99 (MQ=255)                                       aTCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGacc                      >  2:1595648/1‑99 (MQ=255)                                       aTCCTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGacc                      <  2:591473/101‑3 (MQ=255)                                         ccTGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAg                    <  1:387059/101‑1 (MQ=255)                                           tGATAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGtt                  <  1:154656/101‑1 (MQ=255)                                              tAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCt               <  2:1625755/101‑1 (MQ=255)                                              tAAATATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCt               <  2:1560666/101‑1 (MQ=255)                                               aaaTATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTg              <  1:998209/101‑1 (MQ=255)                                                aaTATCCATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTgg             <  2:1059682/101‑1 (MQ=255)                                                      cATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaa       <  2:1297011/101‑1 (MQ=255)                                                      cATGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaa       <  2:192131/101‑1 (MQ=255)                                                       aTGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaaa      <  2:896212/101‑1 (MQ=255)                                                        tGAACGCAAAAATCAGATACGGCCTGTCGTCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaaaa     >  1:874994/1‑101 (MQ=255)                                                        tGAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGaaaaa     <  1:434989/101‑1 (MQ=255)                                                         gAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAag    >  2:640000/1‑101 (MQ=255)                                                         gAACGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAag    <  1:371834/101‑1 (MQ=255)                                                           aCGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGGTTGCCGCCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAagaa  <  2:820048/101‑2 (MQ=255)                                                           aCGCAAAAATCAGATACGGCCTGTCGGCTGCCGTTCTGGCACTGATTGCCGTCGGTGCGCCTGCGCCTGATATTCTCGACCAGTTTCTGGATGAAAAagaa  <  2:672587/101‑2 (MQ=255)                                                              |                                                                                                  GGTAAGATTTAACATATCCGGGGATTTGAAGCCGATAAATCCTGATAAATATCCATGAACGTAAAAATCAGATACAGCCTGTCGGCCGCTGTTCTGGCACTGATTGCCGCCAGTGCTCCTGCCCCTGACATTCTCGATCAGTTTCTGGATGAAAAAGAG  >  178/898‑1056

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑