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
A8 F1 I1 R1 771 44.8 2153074 94.1% 2026042 109.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,034,536 G→A pseudogene (486/663 nt) yedS → pseudogene, outer membrane protein homology, putative outer membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,034,5360GA100.0% 175.9 / NA 55pseudogene (486/663 nt)yedSpseudogene, outer membrane protein homology, putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/24);  total (31/24)

AGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTCAAC  >  NC_000913/2034416‑2034670
                                                                                                                        |                                                                                                                                      
aGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActtt                                                                                                                      >  2:1025591/1‑139 (MQ=255)
  aaGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                                    >  2:286164/1‑139 (MQ=255)
      aTGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgctttg                                                                                                                <  1:1025591/139‑1 (MQ=255)
       tGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACtttgctttgc                                                                                                               >  1:52323/1‑139 (MQ=255)
         gACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTGGCTTTGCaa                                                                                                             >  2:634086/1‑139 (MQ=255)
            cGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                          <  1:74382/139‑1 (MQ=255)
                  gctgcCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                                    <  1:522394/139‑1 (MQ=255)
                        aGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTaataat                                                                                              >  2:457257/1‑139 (MQ=255)
                                gtggCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                    >  2:400838/1‑93 (MQ=255)
                                gtggCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                    <  1:400838/93‑1 (MQ=255)
                                    cGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAg                                                                                         <  1:5209/132‑1 (MQ=255)
                                    cGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAg                                                                                         >  2:5209/1‑132 (MQ=255)
                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACGATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTCTGCAATATCAGGGTAATAATGAAAGCGGTGGACCATTCGGGCAGGaa                                                                   >  1:632517/1‑139 (MQ=255)
                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                    <  2:1018689/74‑1 (MQ=255)
                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                    >  1:1018689/1‑74 (MQ=255)
                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                                    <  2:665241/106‑1 (MQ=255)
                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                                    >  1:665241/1‑106 (MQ=255)
                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                                   >  2:598755/1‑139 (MQ=255)
                                                   cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                                   >  2:390646/1‑139 (MQ=255)
                                                      tGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGATTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGt                                                                >  1:106610/1‑139 (MQ=255)
                                                       gACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGa                                                                                            <  1:328145/110‑1 (MQ=255)
                                                       gACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGa                                                                                            >  2:328145/1‑110 (MQ=255)
                                                       gACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGtt                                                               >  2:26467/1‑139 (MQ=255)
                                                           aCTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCgg                                                           <  1:634086/139‑1 (MQ=255)
                                                             ttCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTa                                                         <  1:390646/139‑1 (MQ=255)
                                                                    aCGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCg                                                            <  1:1071859/129‑1 (MQ=255)
                                                                    aCGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCg                                                            >  2:1071859/1‑129 (MQ=255)
                                                                       gTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                    >  2:593362/1‑54 (MQ=255)
                                                                       gTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                    <  1:593362/54‑1 (MQ=255)
                                                                        tCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                          <  2:830264/79‑1 (MQ=255)
                                                                        tCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                          >  1:830264/1‑79 (MQ=255)
                                                                          gTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                        <  1:429015/63‑1 (MQ=255)
                                                                          gTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                        >  2:429015/1‑63 (MQ=255)
                                                                           tGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGt                                           >  1:1031315/1‑139 (MQ=255)
                                                                                  ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                                    <  1:991429/75‑1 (MQ=255)
                                                                                  ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                                    >  2:991429/1‑75 (MQ=255)
                                                                                  ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTc                                                              <  2:210354/113‑1 (MQ=255)
                                                                                  ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTc                                                              >  1:210354/1‑113 (MQ=255)
                                                                                      ttGCAACCTACGGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTAGCTTTGCAATATCAGGGTAATAATGAAAGtggtgg                                                                                   >  2:622400/1‑88 (MQ=255)
                                                                                      ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGtggtgg                                                                                   <  1:622400/88‑1 (MQ=255)
                                                                                      ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGc                                        >  1:605184/1‑131 (MQ=255)
                                                                                      ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGc                                        <  2:605184/131‑1 (MQ=255)
                                                                                      ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCaa                                >  2:780937/1‑139 (MQ=255)
                                                                                              tACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATg                        >  1:664666/1‑139 (MQ=255)
                                                                                                 cGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTg                     <  1:780937/139‑1 (MQ=255)
                                                                                                      cAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAgg                                                                                                      <  2:505030/53‑1 (MQ=255)
                                                                                                      cAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAgg                                                                                                      >  1:505030/1‑53 (MQ=255)
                                                                                                        aTGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGttt              >  1:626695/1‑139 (MQ=255)
                                                                                                        aTGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGttt              >  1:960081/1‑139 (MQ=255)
                                                                                                           gCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                          <  2:1017174/44‑1 (MQ=255)
                                                                                                           gCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                          >  1:1017174/1‑44 (MQ=255)
                                                                                                           gCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCgg           <  1:450400/139‑1 (MQ=255)
                                                                                                                 ttGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTc     >  1:478654/1‑139 (MQ=255)
                                                                                                                   ggTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTCaa   <  2:664666/139‑1 (MQ=255)
                                                                                                                    gTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTCAAc  <  1:854514/139‑1 (MQ=255)
                                                                                                                        |                                                                                                                                      
AGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTCAAC  >  NC_000913/2034416‑2034670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A