Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A17 F25 I40 R1 5 43.7 1427114 97.2% 1387154 146.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP009273 2,860,429 Δ1 bp coding (482/993 nt) rpoS ← RNA polymerase, sigma S (sigma 38) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,860,4270T.100.0% 183.3 / NA 41coding (484/993 nt)rpoSRNA polymerase, sigma S (sigma 38) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (28/13);  total (28/13)

AACTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAA  >  CP009273/2860293‑2860555
                                                                                                                                      |                                                                                                                                
aaCTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATGGGCAAACGAATGATACGGG‑GTGGTGCATAATCGc                                                                                                                   >  2:70503/1‑149 (MQ=255)
aaCTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATCGTACGGG‑TTGGTTCATAATCGc                                                                                                                   >  2:114970/1‑149 (MQ=255)
aaCTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGc                                                                                                                   >  2:137170/1‑149 (MQ=255)
     gCTTATCCAGTTGCTGTGCGATCGCTTCCGCACTTGGTTAATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCCGCAAACGAATAGTCCGCG‑TTGGTTCATAATCgt                                                                                                                   >  1:81229/1‑143 (MQ=255)
        tATCCCGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCGTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCg                                                                                                                <  1:371044/144‑1 (MQ=255)
             aGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTCCGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGtt                                                                                                      >  2:193492/1‑148 (MQ=255)
                 gCTCTGCGATCTTTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGc                                                                                                  <  2:24729/149‑1 (MQ=255)
                     tGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTAATAATCGCCCGTTCAATCGTCTGGCGAAt                                                                                              >  2:303606/1‑149 (MQ=255)
                        gATCTCTTCCGCACGTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGa                                                                                                >  1:391194/1‑144 (MQ=255)
                            tctTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAg                                                                                       >  2:681543/1‑149 (MQ=255)
                               tCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCACCCGTTCAATCGTCTGGCGAATCCACCAGGtt                                                                                    >  2:377231/1‑149 (MQ=255)
                                                gTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTgag                                                                        <  1:104709/144‑1 (MQ=255)
                                                   cAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGaa                                                                >  2:600963/1‑149 (MQ=255)
                                                        tATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCCGGTTGCGTATGTTGGGAAGCGGaa                                                                >  1:441496/1‑144 (MQ=255)
                                                                aaCTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGtt                                                        >  1:206586/1‑144 (MQ=255)
                                                                aaCTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCggg                                                   >  2:74110/1‑149 (MQ=255)
                                                                 tcTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTc                                                       <  1:555614/143‑1 (MQ=255)
                                                                  cTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTc                                                 <  2:572688/149‑1 (MQ=255)
                                                                   tCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAAGGAATAGTACGGG‑TTGGTTTATAATCGCCCGTTCAATCGTCTGGCCGATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGGTCCg                                                     >  1:441940/1‑144 (MQ=255)
                                                                   tCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCCGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGGCa                                                >  2:613575/1‑149 (MQ=255)
                                                                     aCGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAGACCACGTTCAGGGTCaaa                                              >  2:336283/1‑149 (MQ=255)
                                                                     aCGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCaaa                                              >  2:117348/1‑149 (MQ=255)
                                                                       gTGCGGTTGGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTc                                                 <  1:207411/144‑1 (MQ=255)
                                                                          cGGTTCGCAGGTACACGTTCAGCTCCCTCACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTtct                                         <  2:622703/149‑1 (MQ=255)
                                                                             ttCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCCCGTTCCGGGTCAACCtt                                           >  1:299164/1‑144 (MQ=255)
                                                                             ttCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACtt                                           <  1:338186/144‑1 (MQ=255)
                                                                               cGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTtct                                         >  1:176326/1‑144 (MQ=255)
                                                                                    gTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACcgcgcg                               <  2:558275/149‑1 (MQ=255)
                                                                                    gTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACcgcgcg                               <  2:487020/149‑1 (MQ=255)
                                                                                          gTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCGAACTTCTCTACCGCGCgg                              >  1:189191/1‑144 (MQ=255)
                                                                                                         gATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTg               >  1:591119/1‑144 (MQ=255)
                                                                                                         gATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCctc          <  2:193575/149‑1 (MQ=255)
                                                                                                         gATGTGAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCAACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGcccac          >  2:250898/1‑147 (MQ=255)
                                                                                                            gtgAATCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGcac            >  1:235771/1‑142 (MQ=255)
                                                                                                                aTCGGCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGACGCGGAAACCACGTTCCGGGTCAAACTTCTCGACCGCGCGGATCAGCCCCAGGTTGCCctcct        >  1:280214/1‑142 (MQ=255)
                                                                                                                 tctgCAAACGAATAGTACGGG‑TTGGTTCATACTCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTc       <  1:32254/141‑1 (MQ=255)
                                                                                                                  cGGCAAACGAATAGGACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCg      <  1:66978/144‑1 (MQ=255)
                                                                                                                    gCAAACGAATAGTACGGG‑TTGGTTCATAATGGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTACGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGAGCCGCCCCAGGGTCCCCTCTTCGAt    >  1:537024/1‑144 (MQ=255)
                                                                                                                    gCAAACGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGAt    >  1:606706/1‑144 (MQ=255)
                                                                                                                    gCAAACGAATAGTACGGG‑TTGGTGCATAATAGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACGACGTTCCGGGTCGAACTTCTCTACCGCGCGGATCAGCCCCCGGTTGCCCTCTTCGAt    >  1:463631/1‑144 (MQ=255)
                                                                                                                      aaaCGAATAGTACGGG‑TTGGTTCATAATCGCCCGTTCAAGCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGGAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGCTGCCCCCTTCGATaa  >  1:8600/1‑144 (MQ=255)
                                                                                                                                      |                                                                                                                                
AACTGGCTTATCCAGTTGCTCTGCGATCTCTTCCGCACTTGGTTCATGGTCCAGCTTATGGGACAACTCACGTGCGGTTCGCAGGTAAACGTTCAGCTCCTTTACGATGTGAATCGGCAAACGAATAGTACGGGTTTGGTTCATAATCGCCCGTTCAATCGTCTGGCGAATCCACCAGGTTGCGTATGTTGAGAAGCGGAAACCACGTTCCGGGTCAAACTTCTCTACCGCGCGGATCAGCCCCAGGTTGCCCTCTTCGATAA  >  CP009273/2860293‑2860555

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A