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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,589,535 C→T I647I (ATC→ATT)  acrD → aminoglycoside/multidrug efflux system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,589,5350CT100.0% 156.0 / NA 48I647I (ATC→ATT) acrDaminoglycoside/multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/26);  total (22/26)

ACATCATGTCGGTGTTTGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATCGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGAGTTGCAGGACCACGCTGGAG  >  NC_000913/2589405‑2589659
                                                                                                                                  |                                                                                                                            
acaTCATGTCGGTGTTTGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCg                                                                                                                         <  2:264260/136‑1 (MQ=255)
acaTCATGTCGGTGTTTGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCg                                                                                                                         >  1:264260/1‑136 (MQ=255)
    catGTCGGTGTTTGCCACCGTTGCTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACg                                                                                                                  >  1:134694/1‑139 (MQ=255)
           gtgtTTGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGt                                                                                                           >  1:435835/1‑139 (MQ=255)
              tttGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTg                                                                                                                       <  2:928282/124‑1 (MQ=255)
              tttGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTAGTTTGCCATTATTGAGCGTg                                                                                                                       >  1:928282/1‑124 (MQ=255)
                tGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCGTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAAc                                                                                                      <  2:971929/139‑1 (MQ=255)
                tGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAAc                                                                                                      <  1:590968/139‑1 (MQ=255)
                        ttGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTaa                                                                                              <  1:1013077/139‑1 (MQ=255)
                        ttGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTaa                                                                                              >  1:833419/1‑139 (MQ=255)
                             tCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAaagaag                                                                                         <  2:833419/139‑1 (MQ=255)
                                ggCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTc                                                                                      >  1:95327/1‑139 (MQ=255)
                                 gCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGTGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCaa                                                                                                   <  1:1234500/125‑1 (MQ=255)
                                 gCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGTGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCaa                                                                                                   >  2:1234500/1‑125 (MQ=255)
                                     tGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGtt                                                                                 <  2:95327/139‑1 (MQ=255)
                                     tGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGtt                                                                                 <  2:435835/139‑1 (MQ=255)
                                            aaCGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCg                                                                                                                         >  2:1236916/1‑92 (MQ=255)
                                            aaCGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCg                                                                                                                         <  1:1236916/92‑1 (MQ=255)
                                                ggCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCcagcag                                                                      <  1:58392/139‑1 (MQ=255)
                                                 gCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCagcagc                                                                     >  1:1181785/1‑139 (MQ=255)
                                                                           gCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAg                                           >  1:28518/1‑139 (MQ=255)
                                                                             cTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAAc                                                                                                      >  1:763851/1‑78 (MQ=255)
                                                                             cTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAAc                                                                                                      <  2:763851/78‑1 (MQ=255)
                                                                             cTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGtt                                         >  1:1419632/1‑139 (MQ=255)
                                                                             cTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGtt                                         <  2:1033610/139‑1 (MQ=255)
                                                                                aaaGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCg                                                                                                                         <  1:444360/56‑1 (MQ=255)
                                                                                aaaGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGACATTATTGAGCg                                                                                                                         >  2:444360/1‑56 (MQ=255)
                                                                                          gCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGa                            >  2:393337/1‑139 (MQ=255)
                                                                                               cgcgACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTaa                                                                                              <  1:852509/68‑1 (MQ=255)
                                                                                               cgcgACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTaa                                                                                              >  2:852509/1‑68 (MQ=255)
                                                                                               cgcgACAGTAAGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATgg                       <  2:134694/139‑1 (MQ=255)
                                                                                                         aGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGAGTTGCAGGa             <  2:28518/139‑1 (MQ=255)
                                                                                                         aGACCGGCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGAGTTGCAGGa             <  1:16090/139‑1 (MQ=255)
                                                                                                               gCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTc                                                                                      <  1:1465308/60‑1 (MQ=255)
                                                                                                               gCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTc                                                                                      >  2:1465308/1‑60 (MQ=255)
                                                                                                               gCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGc                                                      <  1:1491966/92‑1 (MQ=255)
                                                                                                               gCACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGc                                                      >  2:1491966/1‑92 (MQ=255)
                                                                                                                cACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAAc                                                                                                      >  2:183446/1‑43 (MQ=255)
                                                                                                                cACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAAc                                                                                                      <  1:183446/43‑1 (MQ=255)
                                                                                                                cACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCaa                                                                                                   >  2:930923/1‑46 (MQ=255)
                                                                                                                cACCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCaa                                                                                                   <  1:930923/46‑1 (MQ=255)
                                                                                                                 aCCTCGTTTGCCCTTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCGGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGa                      <  1:1038887/122‑1 (MQ=255)
                                                                                                                 aCCTCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGa                      >  2:1038887/1‑122 (MQ=255)
                                                                                                                    tCGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGAGTTGCAGGACCACGCTGGAg  <  1:393337/139‑1 (MQ=255)
                                                                                                                     cGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGata                          >  1:546612/1‑114 (MQ=255)
                                                                                                                     cGTTTGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGata                          <  2:546612/114‑1 (MQ=255)
                                                                                                                         tGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCg                                                     >  1:1001641/1‑83 (MQ=255)
                                                                                                                         tGCCATTATTGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCg                                                     <  2:1001641/83‑1 (MQ=255)
                                                                                                                             attattGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGcc                                                                >  2:146290/1‑68 (MQ=255)
                                                                                                                             attattGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGcc                                                                <  1:146290/68‑1 (MQ=255)
                                                                                                                             attattGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTg                                      >  2:1228212/1‑94 (MQ=255)
                                                                                                                             attattGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTg                                      <  1:1228212/94‑1 (MQ=255)
                                                                                                                                  |                                                                                                                            
ACATCATGTCGGTGTTTGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATCGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGAGTTGCAGGACCACGCTGGAG  >  NC_000913/2589405‑2589659

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A