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
A4 F50 I2 R1 104 44.1 1376607 98.9% 1361464 150.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 599,828 T→C L372P (CTG→CCG)  cusA → copper/silver efflux system, membrane component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,8280TC100.0% 147.4 / NA 43L372P (CTG→CCG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/23);  total (20/23)

ACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCTGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCATAAACGGCTGGAAGAGTG  >  NC_000913/599680‑599975
                                                                                                                                                    |                                                                                                                                                   
acaacaTACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCgg                                                                                                                                                   >  1:333259/1‑151 (MQ=255)
       aCGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTtgt                                                                                                                                             <  2:668578/150‑1 (MQ=255)
        cGATCGCAGCCAGCTCATTGACCGCGCCATCGCCAACCTCAGCGGCAAGTTGCTGGAAGAGATTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGtt                                                                                                                                               >  1:636628/1‑147 (MQ=255)
        cGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTtgt                                                                                                                                             >  1:197284/1‑149 (MQ=255)
         gATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTa                                                                                                                                          <  1:178254/151‑1 (MQ=255)
          aTCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGCGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTAt                                                                                                                                         >  1:364115/1‑151 (MQ=255)
           acGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGGAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGGGGCGATTATTTCGTTGCCGCCGGGGGTGTGGAtt                                                                                                                                        >  1:252876/2‑151 (MQ=255)
            cGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTg                                                                                                                                       >  2:405081/1‑151 (MQ=255)
              cagccagcTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCt                                                                                                                                     <  2:78670/151‑1 (MQ=255)
                    gcTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTAtt                                                                                                                               <  2:395412/151‑1 (MQ=255)
                         ttGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCAt                                                                                                                          >  2:599248/1‑151 (MQ=255)
                                 gcCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTcc                                                                                                                  >  2:296698/1‑151 (MQ=255)
                                  ccATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATTTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCGCTTCCa                                                                                                                 <  1:617219/151‑1 (MQ=255)
                                      cGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAggg                                                                                                              <  2:243282/150‑1 (MQ=255)
                                         cAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTg                                                                                                          <  2:160002/151‑1 (MQ=255)
                                          aaCCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGGAGTCTGTGCGCTGTTTCCCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCCGGGACTg                                                                                                          >  1:484868/1‑150 (MQ=255)
                                            ccTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAAt                                                                                                       >  1:656772/1‑151 (MQ=255)
                                               cAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATg                                                                                                      <  2:683024/149‑1 (MQ=255)
                                                   ggCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAata                                                                                                <  1:66540/151‑1 (MQ=255)
                                                       aGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTa                                                                                                                                 <  1:130096/114‑1 (MQ=255)
                                                       aGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAAtattat                                                                                            >  1:128238/1‑151 (MQ=255)
                                                       aGTTGCTGGAAGAGTTTATTGTGGGGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTa                                                                                                                                 >  2:130099/1‑114 (MQ=255)
                                                              ggAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGGATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGt                                                                                       >  2:309517/1‑149 (MQ=255)
                                                                  gagTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTg                                                                                 <  1:579476/151‑1 (MQ=255)
                                                                        aTTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTg                                                                           <  2:255549/151‑1 (MQ=255)
                                                                          tgtgGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGc                                                                          <  1:401509/150‑1 (MQ=255)
                                                                             ggtggCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGAt                                                                       <  1:176530/150‑1 (MQ=255)
                                                                              gtggCGGTAGTCTGTGCGCTGTTTTTCTGGGATGTGCGCCCGGCGCTCGGGGCGGGTATTTTGTTGCCGCCGGGGGTGTGTATTGCTTTTATTTTCATTCACTTCCAGGGGCTGGATGCCCATATTATGTCGTTGGGTGGCAttttccgt                                                                      >  1:572122/1‑144 (MQ=255)
                                                                                      aGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCgg                                                              <  2:269481/150‑1 (MQ=255)
                                                                                           gtgCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCg                                                          <  1:405068/149‑1 (MQ=255)
                                                                                             gcgcTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATg                                                       <  1:275465/150‑1 (MQ=255)
                                                                                                cTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCg                                                   >  2:529509/1‑151 (MQ=255)
                                                                                                                     tCGGCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCg                              >  2:310549/1‑151 (MQ=255)
                                                                                                                       ggCGCTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCgag                            <  2:512038/151‑1 (MQ=255)
                                                                                                                        gcgcTGGTGGCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCg                              >  2:219246/1‑148 (MQ=255)
                                                                                                                             ggtggCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATg                        <  2:436225/149‑1 (MQ=255)
                                                                                                                               tggCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATgcgc                     >  2:129476/1‑150 (MQ=255)
                                                                                                                                ggCGATTATTTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCAt                   <  1:354037/151‑1 (MQ=255)
                                                                                                                                       attTCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCATAAACgg             <  1:12654/150‑1 (MQ=255)
                                                                                                                                         ttCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCATAAACGGCt           <  1:547548/150‑1 (MQ=255)
                                                                                                                                         ttCGTTGCCGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCATAAACGGCt           <  2:619431/150‑1 (MQ=255)
                                                                                                                                                 cGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCATAAACGGCTGGAAGAGTg  >  2:606000/1‑151 (MQ=255)
                                                                                                                                                 cGCCGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCATAAACGGCTGGAAGAGTg  >  1:551049/1‑151 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
ACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTTGCCGCTGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAATATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTCATGATCGAGAATGCGCATAAACGGCTGGAAGAGTG  >  NC_000913/599680‑599975

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A