Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,257,010 A→T 10.3% noncoding (305/451 nt)
F41I (TTC→ATC) 		 PP_mr14 ←
capB ←		 cspA regulatory region
cold shock protein CapB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,257,0100AT10.3% 97.0 / 4.0 39noncoding (305/451 nt)
F41I (TTC→ATC) 		PP_mr14
capB		cspA regulatory region
cold shock protein CapB
Reads supporting (aligned to +/- strand):  ref base A (18/17);  new base T (2/2);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.10e-01

AGGCATAAAAAAACCCGCCAGAAGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACGGTTGGACATTTTTCTGTCTCCTTGGACAATTTGAT  >  NC_002947/1256862‑1257156
                                                                                                                                                    |                                                                                                                                                  
aGGCATAAAAAAACCCGCCAGAAGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGCCGATCTCAACTTCTTCAGCCTGCATGCGTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGaa                                                                                                                                                    >  4:283363/1‑149 (MQ=255)
   cATAAAAAAACCCGCCAGAAGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGCACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCTGGGGTTTGAAGcg                                                                                                                                                 >  3:169448/1‑148 (MQ=255)
    aTAAAAAAACCCGCCAGAAGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCg                                                                                                                                                >  1:228380/1‑149 (MQ=255)
    aTAAAAAAACCCGCCAGAAGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCg                                                                                                                                                >  5:294537/1‑149 (MQ=255)
                 ccAGAAGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATgg                                                                                                                                   >  2:24722/1‑149 (MQ=255)
                      aGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTg                                                                                                                              <  5:322868/149‑1 (MQ=255)
                        gCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGaa                                                                                                                            >  3:186690/1‑149 (MQ=255)
                          gggTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGt                                                                                                                          <  4:186690/149‑1 (MQ=255)
                           ggTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTg                                                                                                                         <  1:321618/149‑1 (MQ=255)
                               tttttGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCAc                                                                                                                      <  3:22281/148‑1 (MQ=255)
                               tttttGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCAc                                                                                                                      <  4:43633/148‑1 (MQ=255)
                                   tGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAAc                                                                                                                  <  6:91944/148‑1 (MQ=255)
                                       aGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGgtc                                                                                                             <  3:314887/149‑1 (MQ=255)
                                              aaGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGccc                                                                                                      <  6:294537/149‑1 (MQ=255)
                                                     aTCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGaa                                                                                                                                                    <  3:276552/96‑1 (MQ=255)
                                                     aTCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGaa                                                                                                                                                    >  4:276552/1‑96 (MQ=255)
                                                        gACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAgggg                                                                                            >  5:65643/1‑149 (MQ=255)
                                                        gACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAggg                                                                                             <  1:24722/148‑1 (MQ=255)
                                                           ttAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGtga                                                                                         >  7:232987/1‑149 (MQ=255)
                                                           ttAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGtga                                                                                         >  8:113540/1‑149 (MQ=255)
                                                             aGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGtgat                                                                                        <  1:36644/148‑1 (MQ=255)
                                                                cGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAg                                                                                    <  8:232987/149‑1 (MQ=255)
                                                                cGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAg                                                                                    <  7:281706/149‑1 (MQ=255)
                                                                      gAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGCTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAg                                                                              >  5:234702/1‑149 (MQ=255)
                                                                             ttcAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGATGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTtct                                                                       >  4:126843/1‑149 (MQ=255)
                                                                             ttcAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAggg                                                                                             >  3:224586/1‑127 (MQ=255)
                                                                             ttcAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAggg                                                                                             <  4:224586/127‑1 (MQ=255)
                                                                             ttcAGCCGGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGATGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTtct                                                                       >  8:80274/1‑149 (MQ=255)
                                                                               cAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTtc                                                                        <  6:65643/146‑1 (MQ=255)
                                                                                  ccTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGATGCGGGAGCGTTtcgggtcg                                                                  >  4:229416/1‑143 (MQ=255)
                                                                                           cTTTCTGGCCGCGTGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCCTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCAc                                                         <  2:228380/149‑1 (MQ=255)
                                                                                                  gCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGATGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTaac                                                    <  3:126843/147‑1 (MQ=255)
                                                                                                  gCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGATGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTaac                                                    <  7:80274/147‑1 (MQ=255)
                                                                                                    cgcgGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTaacaa                                                  >  5:187038/1‑147 (MQ=255)
                                                                                                    cgcgGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTaacaa                                                  <  6:187038/147‑1 (MQ=255)
                                                                                                                       aaCAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACGGTTGGACa                             >  8:83954/1‑149 (MQ=255)
                                                                                                                        aCAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCTTCGTTGAACCACTTAACAACACCGGATTGACGGTTGGACAt                            >  5:292493/1‑149 (MQ=255)
                                                                                                                        aCAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACgg                                    <  7:270477/141‑1 (MQ=255)
                                                                                                                        aCAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACgg                                    >  8:270477/1‑141 (MQ=255)
                                                                                                                                 ccTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAAGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACGGTTGGACATTTTTCTGtc                   >  8:63323/1‑149 (MQ=255)
                                                                                                                                      tttCAGAGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCAAGAACAGGTCGTCGCCCGACTGAGGGGTGATTAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGAATTCAAGGTTGGACATTTATATCTCTCCtt              >  4:105017/1‑149 (MQ=25)
                                                                                                                                           gggTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACGGTTGGACATTTTTCTGTCTCCTTGGAc          >  1:67603/1‑148 (MQ=255)
                                                                                                                                                   aaGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACGGTTGGACATTTTTCTGTCTCCTTGGACAATTTGAt  >  2:24110/1‑148 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
AGGCATAAAAAAACCCGCCAGAAGGCGGGTTTTTTTGAAAGCTAGGAAGCTAGATCGACTTAGGCGATCTGAACTTCTTCAGCCTGCATGCCTTTCTGGCCGCGGGTAGCGACGAAAGTAACAGCCTGGCCTTCTTTCAGGGTTTTGAAGCCGTCAGCTTGGATGGCTTTGAAGTGCACGAACAGGTCGTCGCCCGACTGAGGGGTGATGAAGCCGTAGCCTTTCTCATCGTTGAACCACTTAACAACACCGGATTGACGGTTGGACATTTTTCTGTCTCCTTGGACAATTTGAT  >  NC_002947/1256862‑1257156

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: ‑