Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,111,713	T→A	10.4%	V181D (GTC→GAC)	PP_3617 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,111,713	0	T	A	10.4%	120.5 / 6.2	49	V181D (GTC→GAC)	PP_3617	membrane protein
Reads supporting (aligned to +/- strand):  ref base T (19/24);  new base A (3/2);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 6.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.33e-01

ATTTTTAAGCGTACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTGGCGCCAC  >  NC_002947/4111574‑4111855                                                                                                                                            |                                                                                                                                                aTTTTTAAGCGTACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGt                                                                                                                                        >  1:213112/1‑149 (MQ=255)  tttttAAGCGTACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGt                                                                                                                                        <  7:198113/148‑1 (MQ=255)  tttttAAGCGTACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGt                                                                                                                                        <  6:85868/148‑1 (MQ=255)        aGCGTACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCTCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGACATGCTTGACGCCggg                                                                                                                                 <  2:68657/149‑3 (MQ=14)        aGCGTACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAg                                                                                                                                 <  2:213112/149‑1 (MQ=255)            tACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTAt                                                                                                                             <  1:105355/149‑1 (MQ=255)              cGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATgg                                                                                                                           <  3:33997/149‑1 (MQ=255)              cGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATgg                                                                                                                           <  5:337017/149‑1 (MQ=255)                  aTACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAAt                                                                                                                       <  6:177557/149‑1 (MQ=255)                   tACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATa                                                                                                                      >  2:351500/1‑149 (MQ=255)                    aCGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATAc                                                                                                                     >  5:239505/1‑149 (MQ=255)                       gcggcTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCAGCCAAAAGACTGCCTCTGGGTCGCCAGTAACGACCCCACCGCACCCGGCGTCACGCATGTCGCCGAGCGATGGGAATcccgc                                                                                                                  >  3:261990/1‑147 (MQ=14)                        cggcTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTcc                                                                                                                 >  2:288688/1‑149 (MQ=255)                        cggcTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTcc                                                                                                                 <  1:351500/149‑1 (MQ=255)                        cggcTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTcc                                                                                                                 <  6:239505/149‑1 (MQ=255)                            tcatcaTTCAGCACCAGCTATGCCCTCGCCTTCGCACCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACACACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCa                                                                                                             >  5:243986/1‑149 (MQ=255)                               tcatTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACtt                                                                                                          >  6:209269/1‑149 (MQ=39)                                catTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCCAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACATCCGCCACtt                                                                                                          >  6:69409/1‑148 (MQ=255)                                 atTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCa                                                                                                        <  3:331380/149‑1 (MQ=38)                                    cAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATg                                                                                                      <  6:183140/148‑1 (MQ=37)                                       cACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGGCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGAcc                                                                                                  <  4:211806/149‑1 (MQ=25)                                          cAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑Cg                                                                                              <  1:288688/149‑1 (MQ=37)                                                       gCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACGTCGGCCACTTCATGGACCA‑CGGCCCGGACAAACt                                                                                 <  5:69409/149‑1 (MQ=255)                                                         cTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCAACAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCCAGGTATGGGAATACCTCCGCCACTTCATGGACCC‑CGGCCCGGCCCAACTcc                                                                               >  6:302061/1‑149 (MQ=11)                                                               cccccGCCGGGAAGACGGCAGCCTGCATCAAAAAGACAGCCTCTGGGTCGACAGTAACGCACCCCCCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCGACTTCATGGCCCA‑CGGCCCGGCCAAACTCCCcccgc                                                                         >  5:68901/1‑149 (MQ=14)                                                                 cccGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCAAGTCGCCGAGGTAtcg                                                                                                                           >  4:132100/1‑96 (MQ=255)                                                                              cGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTGGACAGTAACGCACCCACCGAACCCGGCGGCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACt                                                          <  5:302061/149‑1 (MQ=255)                                                                                    ccTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGc                                                    <  5:308304/149‑1 (MQ=37)                                                                                       gCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCCAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGcac                                                  >  1:119146/1‑148 (MQ=37)                                                                                        cATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGAGTCAAGCATGTCGCCGAGGTATGGTAATACCTCCGCCACTTCATTGACCA‑CGGCCCTGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACaa                                                <  6:68901/149‑1 (MQ=255)                                                                                         aTCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAg                                               >  5:135328/1‑149 (MQ=35)                                                                                              aaaGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGATGTATGGGAATACCTCCGCCACTTCATGGACCATCGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCAc                                           <  1:282216/149‑1 (MQ=255)                                                                                                  aCTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTACGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCACGGTGAACCCAACTGGTGGCACAAGCCACTGCAc                                      <  6:243986/149‑1 (MQ=21)                                                                                                       ctctGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCa                                  >  2:261531/1‑148 (MQ=34)                                                                                                            ggTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAg                                               >  4:330403/1‑130 (MQ=35)                                                                                                            ggTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAg                                               <  3:330403/130‑1 (MQ=35)                                                                                                                  ccgTAACGAACCCACCTCACCCGGAGTCCAGCATGTAGCCGAGGTATTTGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGAAAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGAcc                       <  4:261990/146‑1 (MQ=11)                                                                                                                     tAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGCACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTCCCCCCgg                   >  4:10412/1‑149 (MQ=255)                                                                                                                     tAACAAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAAc                                                                >  6:217806/1‑104 (MQ=25)                                                                                                                               aCCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCTGa                                                                                       <  3:239406/71‑1 (MQ=21)                                                                                                                               aCCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGa                                                                                       >  4:239406/1‑71 (MQ=34)                                                                                                                                ccGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTgg        >  8:27770/1‑149 (MQ=34)                                                                                                                                 cGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTGgc       <  6:135328/149‑1 (MQ=34)                                                                                                                                   aaCCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTGgcgc     <  3:10412/149‑1 (MQ=34)                                                                                                                                    cctcGGCGACATGCTTGACGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCACCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGACATCTGCCTGACCCAGGCAGAAGCCTCgccc     >  1:351335/4‑146 (MQ=11)                                                                                                                                      tcGGCGACATGCTTGACGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTGgc       <  7:238219/143‑1 (MQ=255)                                                                                                                                      tcGGCGACATGCTTGACGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTGgc       >  8:238219/2‑144 (MQ=255)                                                                                                                                      tcGGCGACATGCTTGACGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTGGCGCCa   >  3:237284/2‑148 (MQ=255)                                                                                                                                      ccGGCGTCAAGCATGTCGCCGATGTATCGGAATACCTCGGCCACTTCATGTACCT‑CGGCCCTGACAAACTCCCCCCGCCCGGTGAACCCAACTGTTGGCACAAGCCAGTGCACGCCATCTGCCTGACCCCGGCAGAAGCATGGCGCCAc  <  8:206607/149‑1 (MQ=11)                                                                                                                                            |                                                                                                                                                ATTTTTAAGCGTACGGAATACGGCGGCTCATCATTCAGCACCAGCTATGCCCTCGCCTTCGCCCCCCGCCGGGAAGACGGCAGCCTGCATCAAAAAGACTGCCTCTGGGTCGACAGTAACGAACCCACCGAACCCGGCGTCAAGCATGTCGCCGAGGTATGGGAATACCTCCGCCACTTCATGGACCA‑CGGCCCGGACAAACTCCCCCCGCCCGGTGAACCCAACTGGTGGCACAAGCCACTGCACGCCATCTGCCTGACCCCGGCAGAAGCCTGGCGCCAC  >  NC_002947/4111574‑4111855

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑