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
A14 F1 I2 R1 70 59.9 2639336 94.5% 2494172 113.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,568,417 C→T G35R (GGG→AGG)  mdtM ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,568,4170CT100.0% 176.0 / NA 51G35R (GGG→AGG) mdtMmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/24);  total (27/24)

CGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAAC  >  NC_000913/4568283‑4568551
                                                                                                                                      |                                                                                                                                       
cGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                     >  2:381575/1‑139 (MQ=255)
          ccAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑t                                                                                                                          <  2:1267794/139‑1 (MQ=255)
          ccAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑t                                                                                                                          <  2:1147748/139‑1 (MQ=255)
               tCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTc                                                                                                                     <  2:753699/139‑1 (MQ=255)
                       aaaGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATa                                                                                                             <  1:1006731/139‑1 (MQ=255)
                        aaGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                     <  2:610345/115‑1 (MQ=255)
                        aaGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATAc                                                                                                            <  2:54177/139‑1 (MQ=255)
                        aaGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATAc                                                                                                            <  2:1004908/139‑1 (MQ=255)
                        aaGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATGAAAATCACGTACCACATTAATGATCCTAGGc                                                                                                                                     >  1:610345/1‑115 (MQ=255)
                            ggCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACgcag                                                                                                        <  1:536387/139‑1 (MQ=255)
                              ccccAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACgcagca                                                                                                      <  1:1076081/139‑1 (MQ=255)
                                       ccACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATAc                                                                                             >  1:482169/1‑139 (MQ=255)
                                            gTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAAt                                                                                        >  1:1019328/1‑139 (MQ=255)
                                                 gCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACg                                                                                   >  1:662061/1‑139 (MQ=255)
                                                          ccAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCg                                                                                                                       >  1:1248692/1‑94 (MQ=255)
                                                          ccAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCg                                                                                                                       <  2:1248692/94‑1 (MQ=255)
                                                          ccAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGcc                                                                                 <  1:1067552/132‑1 (MQ=255)
                                                          ccAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGcc                                                                                 >  2:1067552/1‑132 (MQ=255)
                                                                        aCTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTggcg                                                            >  2:163441/1‑139 (MQ=255)
                                                                           gACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCa                                                         >  1:334830/1‑139 (MQ=255)
                                                                            aCGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAg                                                                                                   >  1:655820/1‑96 (MQ=255)
                                                                            aCGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAg                                                                                                   <  2:655820/96‑1 (MQ=255)
                                                                            aCGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCAt                                                        >  1:59293/1‑139 (MQ=255)
                                                                            aCGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCAGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCCTCGGGAAAAACAGCGTGGCGGCAt                                                        >  1:913486/1‑139 (MQ=255)
                                                                             cGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATg                                                       >  1:985321/1‑139 (MQ=255)
                                                                               gcagcaGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGc                                                     <  2:1308365/139‑1 (MQ=255)
                                                                                cagcagGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGt                                                                                                  >  1:567774/1‑93 (MQ=255)
                                                                                cagcagGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGt                                                                                                  <  2:567774/93‑1 (MQ=255)
                                                                                      gggCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGATTCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTaa                                               >  2:147040/1‑139 (MQ=255)
                                                                                        gCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTaaaaa                                            >  2:968907/1‑139 (MQ=255)
                                                                                           aGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACgcagca                                                                                                      >  2:8374/1‑78 (MQ=255)
                                                                                           aGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACgcagca                                                                                                      <  1:8374/78‑1 (MQ=255)
                                                                                             aCTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGt                                       >  2:1030510/1‑139 (MQ=255)
                                                                                             aCTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGt                                       >  2:406430/1‑139 (MQ=255)
                                                                                              cTGACATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTg                                      <  2:342901/139‑1 (MQ=255)
                                                                                                 aCATCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCa                                   <  1:1247892/139‑1 (MQ=255)
                                                                                                   aTCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATa                                 >  2:307530/1‑139 (MQ=255)
                                                                                                    tCGGCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGCCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaa                                <  1:381575/139‑1 (MQ=255)
                                                                                                      ggCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaaca                              >  2:333594/1‑139 (MQ=255)
                                                                                                       gCATTAAAATCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaa                             >  2:747351/1‑139 (MQ=255)
                                                                                                              aaTCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTc                      <  2:662061/139‑1 (MQ=255)
                                                                                                               aTCACGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                     <  1:1030510/139‑1 (MQ=255)
                                                                                                                  aCGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTc                      >  2:283591/1‑135 (MQ=255)
                                                                                                                  aCGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTc                      <  1:283591/135‑1 (MQ=255)
                                                                                                                  aCGTACCACATTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTg                  >  2:472587/1‑139 (MQ=255)
                                                                                                                        cacaTTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGga            >  2:472256/1‑139 (MQ=255)
                                                                                                                        cacaTTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGga            <  2:946354/139‑1 (MQ=255)
                                                                                                                        cacaTTAATGATCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGga            <  2:985321/139‑1 (MQ=255)
                                                                                                                                  aTCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                     <  1:572257/120‑1 (MQ=255)
                                                                                                                                  aTCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                     >  2:572257/1‑120 (MQ=255)
                                                                                                                                  aTCCTAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAAc  >  1:666638/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                       
CGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGA‑TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAAC  >  NC_000913/4568283‑4568551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A