Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,924,542 T→C 12.5% A41A (GCT→GCC)  PP_5190 → type II secretion system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,924,5420TC12.5% 77.3 / 4.9 32A41A (GCT→GCC) PP_5190type II secretion system protein
Reads supporting (aligned to +/- strand):  ref base T (18/10);  new base C (2/2);  total (20/12)
Fisher's exact test for biased strand distribution p-value = 6.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

ACGCCAACCATGCACACCCCCGACAACCCCGCACTCGACCTCAAGCGCGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACAAGGTCGGCCAACCCTACCTGCGCA  >  NC_002947/5924411‑5924666
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aCGCCAACCATGCACACCCCCGACAACCCCGCACTCGACCTCAAGCGCGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGcc                                                                                                                          >  2:119751/1‑136 (MQ=255)
         aTGCACACCCCCGACAACCCCGCACTCGACCTCAAGCGCGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTgg                                                                                                                 <  2:400955/136‑1 (MQ=255)
                    cGACAACCCCGCACTCGACCTCAAGCGCGTGCTCCAGGCCCTGCTCGCAGACCAGCACCTGCACGCCACCGATACCCTGCAAGTACACGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACCTcgcc                                                                                                      >  1:87320/1‑136 (MQ=255)
                              gCACTCGACCTCAAGCGCGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGcc                                                                                            >  2:420731/1‑136 (MQ=255)
                                       cTCAAGCGCGTGCTCCTGGCCCTGCTCGCGGACCAGCTCCTGCACGCCTGCGATTCCCTGCAAGTACTCTAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAgcc                                                                                   <  2:461962/136‑1 (MQ=255)
                                        tCAAGCGCGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAgccg                                                                                  >  2:31913/1‑136 (MQ=255)
                                            gcgcGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCCAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAg                                                                              >  2:350578/1‑136 (MQ=255)
                                            gcgcGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCCAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAg                                                                              >  2:353591/1‑136 (MQ=255)
                                                         gCCCTGCGCGCTGACCAGCACCTGCACGCCACCGATACCCTGCAAGTACTCTAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGc                                                                 <  2:211014/136‑1 (MQ=255)
                                                          cccTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCCAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGcc                                                                <  1:353591/136‑1 (MQ=255)
                                                          cccTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCCAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGcc                                                                <  1:350578/136‑1 (MQ=255)
                                                             tGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGccccg                                                             >  1:377351/1‑135 (MQ=255)
                                                                tCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGa                                                          >  1:491538/1‑136 (MQ=255)
                                                                 cgatGACAAGAACCTGCACGCCACCGATAGACTGCAAGTACTCGAACAAGCCGCTGACAACACCGCTAGCCACCATCTGGAGCACATAGACGCCTGCAGCCTGGAAATACTACAGCACCCCGGCCAGCCCCTGCAc                                                         >  2:192248/4‑136 (MQ=255)
                                                                 cGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCCCCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGAc                                                         >  2:326063/1‑136 (MQ=255)
                                                                 cGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGTTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGAc                                                         >  2:360801/1‑136 (MQ=255)
                                                                 cGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCg                                                                       >  2:373625/1‑122 (MQ=255)
                                                                 cGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCg                                                                       <  1:373625/122‑1 (MQ=255)
                                                                 cGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGAc                                                         >  1:40934/1‑136 (MQ=255)
                                                                 cGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGAc                                                         >  1:54867/1‑136 (MQ=255)
                                                                 cGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGAc                                                         >  2:288240/1‑136 (MQ=255)
                                                                    tGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTg                                                      <  1:119751/136‑1 (MQ=255)
                                                                    tGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTg                                                      <  2:54867/136‑1 (MQ=255)
                                                                                           aTACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGtggctggc                               >  2:542611/1‑136 (MQ=255)
                                                                                                cTGAAAGTATTGGATCACGCCGCTGCCCACCCCGCTAGCCACCTGCTGGAGCACATCGCCGCCTGCAGCCTGTATAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACa                          <  2:217985/136‑1 (MQ=255)
                                                                                                         ctccaccacGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACAAGGTCGGcc                 <  1:87194/130‑1 (MQ=255)
                                                                                                              acacGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGCCCAGGTCGGCCCAccc            >  1:355609/1‑136 (MQ=255)
                                                                                                                       tGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGCCAAGGTGGGCCACCCCAACCAgcgg   >  1:484295/1‑135 (MQ=255)
                                                                                                                       tGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACAAGGTCGGCCCACCCTACCTgcgc   >  2:458295/1‑136 (MQ=255)
                                                                                                                       tGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACAAGGTCGGCCAACCCTACCAgcgc   >  2:9005/1‑136 (MQ=255)
                                                                                                                        gCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACAAGGTCGGCCAACCCTACCTGCGCa  <  1:288240/136‑1 (MQ=255)
                                                                                                                        gCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACAAGGTCGGCCAACCCTACCTGCGCa  <  1:157467/136‑1 (MQ=255)
                                                                                                                                   |                                                                                                                            
ACGCCAACCATGCACACCCCCGACAACCCCGCACTCGACCTCAAGCGCGTGCTCCAGGCCCTGCTCGCTGACCAGCACCTGCACGCCAGCGATACCCTGCAAGTACTCGAACACGCCGCTGCCCACCCCGCTAGCCACCCGCTGGAGCACATCGCCGCCTGCAGCCTGGAAAGCCGCCAGCACCCCGGCCAGCCCCTGGACTTGGAGCACCTTTGCCAGTGGCTGGCCGACAAGGTCGGCCAACCCTACCTGCGCA  >  NC_002947/5924411‑5924666

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: ‑