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
A2 F1 I2 R1 764 42.0 2018750 95.5% 1927906 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,313,739 (C)5→4 coding (252/2673 nt) rcsD → phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,313,7350C.100.0% 229.1 / NA 54coding (248/2673 nt)rcsDphosphotransfer intermediate protein in two‑component regulatory system with RcsBC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (29/25);  total (29/25)

TACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGG  >  NC_000913/2313600‑2313868
                                                                                                                                       |                                                                                                                                     
tACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTcccc                                                                                                                                    <  1:215449/139‑1 (MQ=255)
 aCAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTcccct                                                                                                                                   >  2:412408/1‑138 (MQ=255)
           gTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGa                                                                                                                        <  1:858049/139‑1 (MQ=255)
             tAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAg                                                                                                                      <  2:581807/139‑1 (MQ=255)
                                aaacGTTACCAGCTTTTCGACAGTACCCATGCTATTAAAAAGTGAGTCAGTAACCGGCGTTACGTGAACTGGTAGATCTACGAGAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCt                                                                                                   <  1:749912/139‑1 (MQ=255)
                                        ccAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAgg                                                                                           <  2:475294/139‑1 (MQ=255)
                                         cAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGa                                                                                          <  2:1008613/139‑1 (MQ=255)
                                                tCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTctac                                                                                   >  2:839395/1‑139 (MQ=255)
                                                              gCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCg                                                                                                                         <  1:290473/87‑1 (MQ=255)
                                                              gCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCg                                                                                                                         >  2:290473/1‑87 (MQ=255)
                                                              gCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                    >  2:601766/1‑124 (MQ=255)
                                                              gCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                    >  2:656571/1‑124 (MQ=255)
                                                              gCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                    <  1:601766/124‑1 (MQ=255)
                                                              gCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                    <  1:656571/124‑1 (MQ=255)
                                                               cTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCa                                                                    <  2:254629/139‑1 (MQ=255)
                                                               cTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCa                                                                    <  2:851428/139‑1 (MQ=255)
                                                                  tCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAg                                                                                            <  1:881788/112‑1 (MQ=255)
                                                                  tCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAg                                                                                            >  2:881788/1‑112 (MQ=255)
                                                                  tCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCAcgc                                                                 >  2:484950/1‑139 (MQ=255)
                                                                  tCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCAcgc                                                                 >  2:583078/1‑139 (MQ=255)
                                                                   ccAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCg                                                                                                                         >  1:735341/1‑82 (MQ=255)
                                                                   ccAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCg                                                                                                                         <  2:735341/82‑1 (MQ=255)
                                                                   ccAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTgg                                                                            >  1:259205/1‑127 (MQ=255)
                                                                   ccAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTgg                                                                            <  2:259205/127‑1 (MQ=255)
                                                                       aaGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCaa                                                            >  2:151292/1‑139 (MQ=255)
                                                                           gcgTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACg                                                        <  2:434684/139‑1 (MQ=255)
                                                                            cgTCGCTAACGGGCGCTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CACCACCTCCGGCGAAGGTTTACAAGAAACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCAGCAAAACgg                                                       >  1:909698/1‑139 (MQ=255)
                                                                            cgTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAAc                                                                                              <  1:851257/100‑1 (MQ=255)
                                                                            cgTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAAc                                                                                              >  2:851257/1‑100 (MQ=255)
                                                                            cgTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACgg                                                       >  1:308875/1‑139 (MQ=255)
                                                                            cgTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACgg                                                       >  2:305806/1‑139 (MQ=255)
                                                                            cgTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACgg                                                       <  2:308875/139‑1 (MQ=255)
                                                                                                  aCCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCa                                 >  1:523366/1‑139 (MQ=255)
                                                                                                  aCCTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCa                                 >  1:736775/1‑139 (MQ=255)
                                                                                                    cTGGCAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACg                               >  2:175892/1‑139 (MQ=255)
                                                                                                        cAGATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACaa                           >  1:350033/1‑139 (MQ=255)
                                                                                                          gATCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACt                         <  2:523366/139‑1 (MQ=255)
                                                                                                           aTCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTc                        <  1:412408/139‑1 (MQ=255)
                                                                                                            tCTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCa                       >  1:784159/1‑139 (MQ=255)
                                                                                                             cTACGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCaa                      >  2:39997/1‑139 (MQ=255)
                                                                                                                cGACAACATTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGc                   <  1:39997/139‑1 (MQ=255)
                                                                                                                      caTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGAt                                                                                         <  2:212069/63‑1 (MQ=255)
                                                                                                                      caTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGAt                                                                                         >  1:212069/1‑63 (MQ=255)
                                                                                                                      caTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                    >  2:335166/1‑68 (MQ=255)
                                                                                                                      caTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                    <  1:335166/68‑1 (MQ=255)
                                                                                                                      caTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCAcgc                                                                 <  2:232422/87‑1 (MQ=255)
                                                                                                                      caTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCAcgc                                                                 >  1:232422/1‑87 (MQ=255)
                                                                                                                      caTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTgaga             >  1:176771/1‑139 (MQ=255)
                                                                                                                       aTTGCCGCGACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGAt            >  2:556402/1‑139 (MQ=255)
                                                                                                                            cgcgACGACCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTc       <  2:784159/139‑1 (MQ=255)
                                                                                                                                acgacCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGa                                                                                                 <  2:344926/45‑1 (MQ=255)
                                                                                                                                acgacCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGa                                                                                                 >  1:344926/1‑45 (MQ=255)
                                                                                                                                acgacCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCg   >  2:372341/1‑139 (MQ=255)
                                                                                                                                acgacCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCg   >  2:298871/1‑139 (MQ=255)
                                                                                                                                acgacCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCg   >  1:982966/1‑139 (MQ=255)
                                                                                                                                 cgacCT‑CCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCgg  <  2:176771/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                     
TACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGG  >  NC_000913/2313600‑2313868

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A