Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	619,820	G→A	8.5%	Q60* (CAG→TAG)	pfeS‑I ←	histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	619,820	0	G	A	8.5%	130.0 / 2.0	47	Q60* (CAG→TAG)	pfeS‑I	histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (20/22);  new base A (2/2);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.15e-01

ATGAATGTCAGGTGGCTGGCTTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACAGGCAGAAGCTGACTTGCA  >  NC_002947/619678‑619960                                                                                                                                               |                                                                                                                                             aTGAATGTCAGGTGGCTGGCTTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGTCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCa                                                                                                                                        >  3:15204/1‑149 (MQ=255)    aaTGTCAGGTGGCTGGCTTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGc                                                                                                                                     <  8:263100/149‑1 (MQ=255)     aTGTCAGGTGGCTGGCTTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGcc                                                                                                                                    >  2:51131/1‑149 (MQ=255)             tggctggcTTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGc                                                                                                                            <  3:100880/149‑1 (MQ=255)               gctggctTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGcc                                                                                                                           <  4:97871/148‑1 (MQ=255)               gctggctTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCt                                                                                                                          >  7:70481/1‑149 (MQ=255)                 tggctTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGt                                                                                                                        <  4:15204/149‑1 (MQ=255)                     ttCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAg                                                                                                                    >  3:145623/1‑149 (MQ=255)                           ggCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTACTCCCACGCCTGTTCGGCCTGTTGAg                                                                                                                    >  1:241739/1‑143 (MQ=255)                           ggCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTACTCCCACGCCTGTTCGGCCTGTTGAg                                                                                                                    <  2:241739/143‑1 (MQ=255)                           ggCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCAAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCCTCCTACTCCCACTCCTGTTCGTCCTGTTGAg                                                                                                                    >  1:247028/1‑143 (MQ=255)                           ggCGCTCAGCGGAGTGGTGCCAAGGATCTGAAGTTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGACCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTACTCCCACGCCTGTTCGGCCTGTTGAg                                                                                                                    <  2:247028/143‑1 (MQ=255)                                              ccAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTcc                                                                                                >  4:39238/1‑144 (MQ=255)                                              ccAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTcc                                                                                                <  3:39238/144‑1 (MQ=255)                                                aaGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAg                                                                                         >  1:331803/1‑149 (MQ=255)                                                  ggCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTAGGCCTGTTCAGCATAACGCGCCAGCTAGTCCTGGTCAGca                                                                                       >  1:40944/1‑148 (MQ=255)                                                   gCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCt                                                                                      <  1:51131/149‑1 (MQ=255)                                                     tctGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTgg                                                                                    <  8:309208/149‑1 (MQ=255)                                                       tGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTgg                                                                                    <  5:107311/147‑1 (MQ=255)                                                       tGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGa                                                                                  >  2:328755/1‑149 (MQ=255)                                                             tgtgGAACTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGaaa                                                                            <  8:150026/149‑1 (MQ=255)                                                                 gACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAg                                                                        <  8:70481/149‑1 (MQ=255)                                                                  aCCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAgg                                                                                                      >  8:17252/1‑118 (MQ=255)                                                                  aCCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAgg                                                                                                      <  7:17252/118‑1 (MQ=255)                                                                  aCCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTgg                                                                                    >  2:250606/1‑136 (MQ=255)                                                                       tCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATa                                                                         >  8:316667/1‑142 (MQ=255)                                                                       tCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATa                                                                         <  7:316667/142‑1 (MQ=255)                                                                       tCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAgg                                                                       >  1:35852/1‑144 (MQ=255)                                                                       tCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAgg                                                                       <  2:35852/144‑1 (MQ=255)                                                                       tCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGCCCTGGTCAGCCTGGGACAGAAAATAGGTACTg                                                                  >  5:372874/1‑149 (MQ=255)                                                                       tCACGGCCACCCAGGTGTACTCGGCCATTGCCACATGCTTGCGCCAGGACTCGGTGCCGGATGCGCCGTACTTCTACCACGCCTGTTAGGACTGTTGAGCATAACTCGCAAGGTAGTCCTGGTCAGACTGGGACATAAAATAGGAACtt                                                                  >  4:65112/1‑148 (MQ=255)                                                                         aCGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCg                                                                >  1:356496/1‑149 (MQ=255)                                                                         aCGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCg                                                                >  6:50874/1‑149 (MQ=255)                                                                               aCCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCAc                                                          <  5:50874/149‑1 (MQ=255)                                                                                 ccAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTgg                                                                                    <  8:46838/121‑1 (MQ=255)                                                                                 ccAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTgg                                                                                    >  7:46838/1‑121 (MQ=255)                                                                                 ccAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCAcc                                                         >  7:224757/1‑148 (MQ=255)                                                                                                       acaTGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAg                                  >  1:58705/1‑149 (MQ=255)                                                                                                        caTGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGc                                 <  4:145623/149‑1 (MQ=255)                                                                                                           gCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGc                                 >  8:238797/1‑146 (MQ=255)                                                                                                               gcgcCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATc                           <  2:58705/148‑1 (MQ=255)                                                                                                                     ggacgcGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTCGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACa                    <  5:218303/144‑1 (MQ=255)                                                                                                                      gCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCTCCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACAg                   <  2:331803/149‑1 (MQ=255)                                                                                                                                cGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACAGGCAGAAGCt          >  4:367237/1‑148 (MQ=255)                                                                                                                                      cgcCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACAGGCAGAAGCTGACTTgc   <  7:238797/149‑1 (MQ=255)                                                                                                                                       gcCGTCCTGCTCCCACGCCTGTTCTGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACAGGCAGAAGCTTACTTgca  <  2:40944/149‑1 (MQ=255)                                                                                                                                       gcCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACAGGCAGAAGCTGACTTgca  <  8:224757/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                             ATGAATGTCAGGTGGCTGGCTTCCTCGGCGCTCAGCGGCGTGGTGCCAAGGCTCTGAAGGTGTGGACCTATCACGGCCACCCAGGTGTCCTCGGCCCGTGCCACATGCTTGCGCCAGGCCTCGGTGCCGGCTGCGCCGTCCTGCTCCCACGCCTGTTCGGCCTGTTGAGCATAACGCGCCAGGTAGTCCTGGTCAGCCTGGGACAGAAAATAGGTACTGCGTTCCACCGAAAGGCCCCAGGTCCAGATGAGCCAGATCAGCAACAGGCAGAAGCTGACTTGCA  >  NC_002947/619678‑619960

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: ‑