Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,854,890	T→A	7.7%	F304I (TTC→ATC)	tcyP →	sodium/cystine symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,854,890	0	T	A	7.7%	153.5 / 2.8	52	F304I (TTC→ATC)	tcyP	sodium/cystine symporter
Reads supporting (aligned to +/- strand):  ref base T (25/23);  new base A (2/2);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

GAGGACATCCTCAAGCTGGGCAGCTTCGTGGTGGTGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCGGGCTCTATCCGGCCA  >  NC_002947/5854743‑5855037                                                                                                                                                    |                                                                                                                                                     gaggaCATCCTCAAGCTGGGCAGCTTCGTGGTGGTGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCtt                                                                                                                                                     >  2:4989/1‑149 (MQ=255)   ggaCATCCTCAAGCTGGGCAGCTTCGTGGTGGTGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCa                                                                                                                                                   >  7:359745/1‑149 (MQ=255)    gaCATCCTCAAGCTGGGCAGCTTCGTGGTGGTGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCAc                                                                                                                                                  <  4:110131/149‑1 (MQ=255)      cATCCTCAAGCTGGGCAGCTTCGTGGTGGTGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCa                                                                                                                                                <  8:359745/149‑1 (MQ=255)            cAAGCTGGGCAGCTTCGTGGTGGTGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCGTTCACCAGCCGCt                                                                                                                                          >  4:112325/1‑149 (MQ=255)                   ggCAGCTTCGTGGTGGGGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAgcgc                                                                                                                                   <  4:233095/149‑1 (MQ=255)                              ggtggtgTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTc                                                                                                                        >  6:82508/1‑149 (MQ=255)                                tggtgTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCg                                                                                                                      <  5:82508/149‑1 (MQ=255)                                    gtCGTACCTGGGCCTGGGTTTGATGTTCGTGGTGCACGGCATCATCATCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCTCCAGCAATCCGCtc                                                                                                                   >  4:302115/1‑147 (MQ=255)                                     tCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGa                                                                                                                  >  1:267683/1‑148 (MQ=255)                                       gTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGCCCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACa                                                                                                               >  4:264648/1‑149 (MQ=255)                                           ctgggcctgggGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATc                                                                                                             >  6:25001/1‑147 (MQ=255)                                              ggcctgggGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAg                                                                                                          <  1:327893/147‑1 (MQ=255)                                                   ggggTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTATTCCGCAAGTTGTGGCCTGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCC‑Caaa                                                                                                  >  7:121400/1‑149 (MQ=255)                                                      tttGATGTTCTTGGTGCACGTCATCATGCTCGCAGCCACCGGCTTGATCACGCTGCGCTTCTTCCTCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGGATTCCGCTGAACATCGAGGCA‑CAAAccc                                                                                               <  8:121400/148‑1 (MQ=255)                                                      gTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAAccc                                                                                               >  3:123058/1‑149 (MQ=255)                                                       ttGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGa                                                                                                           <  4:41581/137‑1 (MQ=255)                                                       ttGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGa                                                                                                           >  3:41581/1‑137 (MQ=255)                                                       ttGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACccg                                                                                              <  2:118575/149‑1 (MQ=255)                                                         gATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACccgcc                                                                                            >  2:225223/1‑149 (MQ=255)                                                            gTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACccgccg                                                                                           >  8:25806/1‑147 (MQ=255)                                                                gtggtgCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTgg                                                                                      <  5:25001/148‑1 (MQ=255)                                                                 tggtgCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGc                                                                                    <  2:267683/149‑1 (MQ=255)                                                                   gtgCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGt                                                                                  >  3:31022/1‑149 (MQ=255)                                                                       aCGGCATCCTCCTCGCAGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCg                                                                              <  4:91813/149‑1 (MQ=255)                                                                          gCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCATCAAACCCGCCGTCTGGGCGTGCCGCa                                                                            <  1:4989/149‑1 (MQ=255)                                                                             tcatcCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGTCGTGCCGCAatcg                                                                        <  8:146879/149‑1 (MQ=255)                                                                                tcCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCATCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAatcgatc                                                                     >  1:271835/1‑149 (MQ=255)                                                                                tcCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCATCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAatcgatc                                                                     >  1:276957/1‑149 (MQ=255)                                                                                   tCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAg                                                                                                                                               <  1:370494/73‑1 (MQ=255)                                                                                   tCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAg                                                                                                                                               >  2:370494/1‑73 (MQ=255)                                                                                    cgccgcCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGc                                                                   >  7:252629/1‑147 (MQ=255)                                                                                     gccgccACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAg                                                                <  8:252629/149‑1 (MQ=255)                                                                                         ccACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCtt                                                             >  3:299693/1‑148 (MQ=255)                                                                                           aCCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCGCTCGATCGCCAGCTTccg                                                          >  6:264494/1‑147 (MQ=255)                                                                                                 gTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATc                                                    <  4:31022/149‑1 (MQ=255)                                                                                                       ccGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCTCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCgg                                              <  5:138307/149‑1 (MQ=255)                                                                                                                    tcCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCtt                                                             <  8:301305/121‑1 (MQ=255)                                                                                                                    tcCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCtt                                                             >  7:301305/1‑121 (MQ=255)                                                                                                                     ccGCAAGGTGTGGCCGGTGCTGACCTTCGCCATCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTg                                   <  2:276957/146‑1 (MQ=255)                                                                                                                     ccGCAAGGTGTGGCCGGTGCTGACCTTCGCCATCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTg                                   <  2:271835/146‑1 (MQ=255)                                                                                                                         aaGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTACAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGaa                            <  3:78949/149‑1 (MQ=255)                                                                                                                                 gCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTgcg                    >  6:270071/1‑149 (MQ=255)                                                                                                                                   cGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCTTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGcc                  <  5:264494/149‑1 (MQ=255)                                                                                                                                   cGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGcc                  >  2:108184/1‑149 (MQ=255)                                                                                                                                      tGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCggg               >  5:165775/1‑149 (MQ=255)                                                                                                                                      tGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCggg               <  8:197563/149‑1 (MQ=255)                                                                                                                                           aCCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCGGGCTCTa          >  7:219450/1‑149 (MQ=255)                                                                                                                                             cTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCGGGCTCTATc        >  1:210196/1‑149 (MQ=255)                                                                                                                                              ttCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCgg                <  8:118652/140‑1 (MQ=255)                                                                                                                                              ttCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCgg                >  7:118652/1‑140 (MQ=255)                                                                                                                                                 gCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCGGGCTCTATCCGGc    <  3:264648/149‑1 (MQ=255)                                                                                                                                                   cTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCGGGCTCTATCCGGCCa  >  4:351619/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GAGGACATCCTCAAGCTGGGCAGCTTCGTGGTGGTGTCGTACCTGGGCCTGGGGTTGATGTTCGTGGTGCACGGCATCATCCTCGCCGCCACCGGCGTGAGCCCGCTGCGCTTCTTCCGCAAGGTGTGGCCGGTGCTGACCTTCGCCTTCACCAGCCGCTCCAGCGCCGCCAGCATTCCGCTGAACATCGAGGCA‑CAAACCCGCCGTCTGGGCGTGCCGCAATCGATCGCCAGCTTCAGCGCATCGTTCGGCACCACCATTGGCCAGAACGGCTGCGCCGGGCTCTATCCGGCCA  >  NC_002947/5854743‑5855037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑