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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,203,224 G→A *67* (TAG→TAA)  croE → e14 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,203,2240GA100.0% 167.2 / NA 52*67* (TAG→TAA) croEe14 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/26);  total (26/26)

TGGTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAGCAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAG  >  NC_000913/1203109‑1203350
                                                                                                                   |                                                                                                                              
tGGTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAAcc                                                                                                         <  2:328470/139‑1 (MQ=255)
  gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTc                                                                                                                    <  2:1447878/126‑1 (MQ=255)
  gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTc                                                                                                                    >  1:1447878/1‑126 (MQ=255)
  gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        >  1:729730/1‑138 (MQ=255)
  gTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        <  2:729730/138‑1 (MQ=255)
        aaTGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACg                                                                                                 >  2:1342425/1‑139 (MQ=255)
          tGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGAt                                                                                               >  1:1171184/1‑139 (MQ=255)
          tGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGAt                                                                                               <  1:304724/139‑1 (MQ=255)
             cTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     <  2:1552938/130‑1 (MQ=255)
             cTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     >  1:1552938/1‑130 (MQ=255)
                        ccAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTgg                                                                                 >  2:1343978/1‑139 (MQ=255)
                          aGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGt                                                                               <  1:1342425/139‑1 (MQ=255)
                           gTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTa                                                                              <  1:806127/139‑1 (MQ=255)
                              ttGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGc                                                                           <  2:1171184/139‑1 (MQ=255)
                                                ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTa                                                                              <  1:1441442/118‑1 (MQ=255)
                                                ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTa                                                                              >  2:1441442/1‑118 (MQ=255)
                                                ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGaa                                                                 >  2:1329960/1‑131 (MQ=255)
                                                ttGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGaa                                                                 <  1:1329960/131‑1 (MQ=255)
                                                       aTACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGcc                                                  >  1:1399590/1‑139 (MQ=255)
                                                           acaTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                              <  1:1343978/139‑1 (MQ=255)
                                                             aTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTg                                                                    <  1:90949/115‑1 (MQ=255)
                                                             aTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTg                                                                    >  2:90949/1‑115 (MQ=255)
                                                             aTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTg                                            >  1:1147989/1‑139 (MQ=255)
                                                              tCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTgg                                           <  2:1399590/139‑1 (MQ=255)
                                                              ataagagacagtACGAAATCTGACTTGAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATGTTTAACCACAGAACGATGAATCTAATCGTAGGTAAGCATCACGTGAAAATAGAAAAACAGCCTGAGTgg                                           <  1:1062943/128‑1 (MQ=255)
                                                                  gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAAttttt                                                                                                             <  2:736196/69‑1 (MQ=255)
                                                                  gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAAttttt                                                                                                             >  1:736196/1‑69 (MQ=255)
                                                                  gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTgg                                           >  2:389591/1‑135 (MQ=255)
                                                                  gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTgg                                           <  1:389591/135‑1 (MQ=255)
                                                                      aaTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGaa                                   <  1:952482/139‑1 (MQ=255)
                                                                       aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAAc                                                                                                          >  2:26519/1‑67 (MQ=255)
                                                                       aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAAc                                                                                                          <  1:26519/67‑1 (MQ=255)
                                                                                  tGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTgg                                                                                 <  1:1215518/81‑1 (MQ=255)
                                                                                  tGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTgg                                                                                 >  2:1215518/1‑81 (MQ=255)
                                                                                    aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCt                               <  1:44008/129‑1 (MQ=255)
                                                                                    aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCt                               >  2:44008/1‑129 (MQ=255)
                                                                                    aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGaaaaa                     >  1:1484235/1‑139 (MQ=255)
                                                                                    aCTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGACTGAGTGGTACGTGAAAGCTGTCAGaaaaa                     >  1:480981/1‑139 (MQ=255)
                                                                                    aCTTAAGACCGGATATCTATCCGAAAGACTAACAGAACACTTTCAATATTTAACCACAAAACGATGACGCTAATCGTGGGTAAGCATGACTGGAAAATAGAAAAACAGCCTGAGTGGTACGCGAAAGcctgtctcttat                     >  2:1062943/1‑128 (MQ=255)
                                                                                              ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        <  1:20523/46‑1 (MQ=255)
                                                                                              ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACca                                                                                                        >  2:20523/1‑46 (MQ=255)
                                                                                              ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     <  2:1115383/49‑1 (MQ=255)
                                                                                              ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAg                                                                                                     >  1:1115383/1‑49 (MQ=255)
                                                                                               gATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCt                                                 <  1:431042/100‑1 (MQ=255)
                                                                                               gATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCt                                                 >  2:431042/1‑100 (MQ=255)
                                                                                                    ctatcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                              >  2:1031753/1‑98 (MQ=255)
                                                                                                    ctatcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                              <  1:1031753/98‑1 (MQ=255)
                                                                                                       tcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATc                                                                                     >  2:681840/1‑56 (MQ=255)
                                                                                                       tcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATc                                                                                     <  1:681840/56‑1 (MQ=255)
                                                                                                       tcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAg  >  2:1650052/1‑139 (MQ=255)
                                                                                                           caaGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAg                                                                            >  1:1043065/2‑61 (MQ=255)
                                                                                                           aaaGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAg                                                                            <  2:1043065/61‑1 (MQ=255)
                                                                                                                   |                                                                                                                              
TGGTTTTCAATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAGCAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAG  >  NC_000913/1203109‑1203350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A