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
A10 F28 I1 R1 180 66.5 2263572 99.4% 2249990 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,604,471 A→G Y142C (TAC→TGC)  lsrD → Autoinducer‑2 ABC transporter membrane subunit LsrD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,604,4710AG100.0% 163.5 / NA 48Y142C (TAC→TGC) lsrDAutoinducer‑2 ABC transporter membrane subunit LsrD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (19/29);  total (19/29)

CGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTACGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGTCTCCTCGTTTTCTGGCTCTGGCTGCATAAA  >  NC_000913/1604334‑1604595
                                                                                                                                         |                                                                                                                            
cGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCg                                                                                                                            >  2:683494/1‑140 (MQ=255)
 ggCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGa                                                                                                                           >  2:1105233/1‑140 (MQ=255)
 ggCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGa                                                                                                                           <  1:558234/140‑1 (MQ=255)
      aTTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTa                                                                                                                      >  1:494422/1‑140 (MQ=255)
       ttGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTAt                                                                                                                     <  2:494422/140‑1 (MQ=255)
             gggCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATtggtgg                                                                                                               <  2:744618/140‑1 (MQ=255)
               gCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGAt                                                                                                             >  2:1034696/1‑140 (MQ=255)
                      aaCGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGAt                                                                                                      <  1:683494/140‑1 (MQ=255)
                      aaCGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGAt                                                                                                      <  1:254191/140‑1 (MQ=255)
                        cGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGCTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATgg                                                                                                    <  2:900429/140‑1 (MQ=255)
                          ccGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCg                                                                                                  >  2:714937/1‑140 (MQ=255)
                              attaattaTCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTa                                                                                              >  1:1073476/1‑140 (MQ=255)
                                       cTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCg                                                                                     <  1:280925/140‑1 (MQ=255)
                                       cTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCg                                                                                     <  1:253261/140‑1 (MQ=255)
                                       cTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCg                                                                                     <  1:153352/140‑1 (MQ=255)
                                          taCCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTa                                                                                  >  2:881730/1‑140 (MQ=255)
                                          taCCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGCGGATTCCCGATGGCGTTTACAGATTTCGc                                                                                    <  2:584146/138‑1 (MQ=255)
                                          taCCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGCGGATTCCCGATGGCGTTTACAGATTTCGc                                                                                    >  1:584146/1‑138 (MQ=255)
                                                aGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTgg                                                                            <  1:871314/140‑1 (MQ=255)
                                                    aaCCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGc                                                                                    <  1:260310/128‑1 (MQ=255)
                                                    aaCCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGc                                                                                    <  2:577083/128‑1 (MQ=255)
                                                    aaCCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGc                                                                                    >  2:260310/1‑128 (MQ=255)
                                                    aaCCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGc                                                                                    >  1:577083/1‑128 (MQ=255)
                                                    aaCCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTGTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGAtgt                                                                        >  2:781236/1‑140 (MQ=255)
                                                    aaCCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCC‑GAAGCGCTCTGCTGTTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGAtgtg                                                                       <  1:282443/140‑1 (MQ=255)
                                                          cTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCC‑GTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGa                                                                 <  1:741164/140‑1 (MQ=255)
                                                           tGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGa                                                                 >  1:993688/1‑140 (MQ=255)
                                                                   aCGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGt                                                         >  1:289610/1‑140 (MQ=255)
                                                                       ttGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCg                                                     <  1:781236/140‑1 (MQ=255)
                                                                       ttGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCg                                                     <  2:188301/140‑1 (MQ=255)
                                                                         ggCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCt                                                   <  1:714937/140‑1 (MQ=255)
                                                                              gCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTa                                              <  2:1073476/140‑1 (MQ=255)
                                                                              gCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTa                                              <  2:993688/140‑1 (MQ=255)
                                                                              gCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTa                                              <  2:1122698/140‑1 (MQ=255)
                                                                              gCTGTATCTGTTTGCCAGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTa                                              <  2:1027180/140‑1 (MQ=255)
                                                                                  tATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCtt                                          <  1:881730/140‑1 (MQ=255)
                                                                                  tATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCtt                                          <  1:1105233/140‑1 (MQ=255)
                                                                                          tGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGatat                                  >  1:86045/1‑140 (MQ=255)
                                                                                            ccGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTa                                              <  1:614743/126‑1 (MQ=255)
                                                                                            ccGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTa                                              >  2:614743/1‑126 (MQ=255)
                                                                                            ccGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCtt                                          <  2:487392/130‑1 (MQ=255)
                                                                                            ccGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCtt                                          >  1:487392/1‑130 (MQ=255)
                                                                                            ccGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGt                                >  2:704005/1‑140 (MQ=255)
                                                                                                      tctGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGTCTCCTCGttt                      >  2:810289/1‑140 (MQ=255)
                                                                                                             ctTTCCGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGTCTCCTCGTTTtctggct               <  1:1034293/140‑1 (MQ=255)
                                                                                                                 ccGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGTCTCCTCGTTTtctggctctgg           <  1:443751/140‑1 (MQ=255)
                                                                                                                  cGGTATGGCCGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGTCTCCTCGTTTtctggctctggc          <  1:401747/140‑1 (MQ=255)
                                                                                                                          ccGGAGCGACGGGGTGCGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGTCTCCTCGTTTTCTGGCTCTGGCTGCATaaa  >  1:651071/1‑140 (MQ=255)
                                                                                                                                         |                                                                                                                            
CGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTGCCGGAAGCGCTCTGCTGCTTTCCGGTATGGCCGGAGCGACGGGGTACGAAGGTATTGGTGGATTCCCGATGGCGTTTACAGATTTCGCTAACCTGGATGTGCTGGGACTCCCCGTTCCGCTGATTATCTTCCTGATATGTCTCCTCGTTTTCTGGCTCTGGCTGCATAAA  >  NC_000913/1604334‑1604595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A