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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,583,454 G→A intergenic (+36/‑29) yrhA → / → insA pseudogene, interrupted by IS1E/IS1 repressor TnpA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,583,4540GA100.0% 146.6 / NA 48intergenic (+36/‑29)yrhA/insApseudogene, interrupted by IS1E/IS1 repressor TnpA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/19);  total (29/19)

ATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATC  >  NC_000913/3583336‑3583564
                                                                                                                      |                                                                                                              
ataGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTTGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAg                                                                                            <  2:236576/139‑1 (MQ=255)
              gatTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCt                                                                              >  2:1135221/1‑139 (MQ=255)
              gatTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCt                                                                              >  1:450630/1‑139 (MQ=255)
                 ttCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                                           >  1:949911/1‑139 (MQ=255)
                      aaaCCCTGAGCTACAAGAACGGTTAGTGAGCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTTCTCCAGTGGCTTCTGTTTc                                                                      >  2:942312/1‑139 (MQ=255)
                           cTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTc                                                                      >  1:897032/1‑134 (MQ=255)
                           cTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTc                                                                      <  2:897032/134‑1 (MQ=255)
                             gATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGc                                                               >  1:269462/1‑139 (MQ=255)
                              aTCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAt                                                                   >  2:645202/1‑134 (MQ=255)
                              aTCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAt                                                                   <  1:645202/134‑1 (MQ=255)
                                  aCAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTcc                                                          <  1:86196/139‑1 (MQ=255)
                                      gAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcctcc                                                      <  2:1288596/139‑1 (MQ=255)
                                        aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                                    >  2:764912/1‑139 (MQ=255)
                                        aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                                    >  2:922679/1‑139 (MQ=255)
                                        aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                                    >  2:160446/1‑139 (MQ=255)
                                        aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGACGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                                    >  2:829685/1‑139 (MQ=255)
                                         cGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGt                                                   >  1:723135/1‑139 (MQ=255)
                                           gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGCTTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTc                                                 >  2:271422/1‑139 (MQ=255)
                                              aGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGc                                              <  2:450630/139‑1 (MQ=255)
                                                 gATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTAc                                           <  2:949911/139‑1 (MQ=255)
                                                    cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCa                                                                                    >  1:379135/1‑95 (MQ=255)
                                                    cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCa                                                                                    <  2:379135/95‑1 (MQ=255)
                                                    cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGa                                        >  1:45257/1‑139 (MQ=255)
                                                    cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGa                                        >  2:1305512/1‑139 (MQ=255)
                                                    cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGa                                        >  1:1163927/1‑139 (MQ=255)
                                                      gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACg                                      <  1:760335/139‑1 (MQ=255)
                                                      gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACg                                      >  2:430869/1‑139 (MQ=255)
                                                           tataGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggtg                                 <  2:45257/139‑1 (MQ=255)
                                                            ataGCATCTCAATATTTACTTATGGCATTAAAGGTGATGCTGCCAACTTACAGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGATACTGACGGggtgg                                >  1:804483/1‑139 (MQ=17)
                                                                     cAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACg                       >  1:209555/1‑139 (MQ=255)
                                                                          tttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaaa                  >  1:1219265/1‑139 (MQ=255)
                                                                          tttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaaa                  >  1:651063/1‑139 (MQ=255)
                                                                           ttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaaaa                 >  2:845543/1‑139 (MQ=255)
                                                                            tACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAg                <  1:1305512/139‑1 (MQ=255)
                                                                            tACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAg                <  1:271422/139‑1 (MQ=255)
                                                                             aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGc               >  2:1239270/1‑139 (MQ=255)
                                                                             aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGc               >  2:1213982/1‑139 (MQ=255)
                                                                             aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGc               >  1:684333/1‑139 (MQ=255)
                                                                              cTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCa              <  1:160446/139‑1 (MQ=255)
                                                                               ttATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTg                                                                                         <  2:974890/63‑1 (MQ=255)
                                                                               ttATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTg                                                                                         >  1:974890/1‑63 (MQ=255)
                                                                               ttATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAc             <  2:209555/139‑1 (MQ=255)
                                                                                  tGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCt                                                                              <  1:280260/71‑1 (MQ=255)
                                                                                  tGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCt                                                                              >  2:280260/1‑71 (MQ=255)
                                                                                         aaaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                           <  2:743542/51‑1 (MQ=255)
                                                                                         aaaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                           >  1:743542/1‑51 (MQ=255)
                                                                                          aaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATc  <  1:942312/139‑1 (MQ=11)
                                                                                          aaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATc  <  1:1239270/139‑1 (MQ=11)
                                                                                                                      |                                                                                                              
ATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATC  >  NC_000913/3583336‑3583564

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