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
A15 F58 I0 R3 247 66.2 2815674 94.9% 2672074 126.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,724,719 G→A 100% D36D (GAC→GAT)  U712_19200 ← SacPA operon antiterminator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,724,7190GA100.0% 128.2 / NA 41D36D (GAC→GAT) U712_19200SacPA operon antiterminator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/14);  total (27/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAGCTGATGATATCCTCAGCTATTTCAATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTAAACTTTTCATTCTCGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTT  >  CP006881/3724597‑3724853
                                                                                                                          |                                                                                                                                      
tAGCTGATGATATCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCttttttt                                                                                                                        >  6:232057/1‑139 (MQ=255)
  gCTGATGATATCCTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTg                                                                                                                       >  3:6852/1‑138 (MQ=255)
             ccTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCTTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATTAGATCATTTTTCTTTTTTTGAAAAGCGATTcc                                                                                                           >  7:60846/1‑139 (MQ=255)
             ccTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTcc                                                                                                           >  2:86213/1‑139 (MQ=255)
             ccTCAGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTcc                                                                                                           >  5:122128/1‑139 (MQ=255)
                 aGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTATGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATAATTTTTCTTTTTTTGAAAAGAGATTcacggt                                                                                                       >  1:137538/1‑134 (MQ=255)
                      tttCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTTTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCAATTTATTCATAGGGATGAGATAATTTTTCTTTTTTTGAAAAGCGATTCCAGGTCCCAt                                                                                                  >  7:298792/1‑139 (MQ=255)
                        tctatatGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGAGCTTTTCCACGTTATTCATAGGGATGAGATCATATTTCTTTTTTGGAAAAGCGATTCCCGGTCCCATCa                                                                                                >  1:308287/4‑139 (MQ=255)
                         ctatatGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCa                                                                                                <  7:12885/136‑1 (MQ=255)
                                   ctccGGCAGTGTTTTCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGAGATTCCCGGTCCCATCAACAttttttag                                                                                     >  3:137764/1‑137 (MQ=255)
                                   ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                     >  7:65058/1‑139 (MQ=255)
                                   ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                     >  3:133587/1‑139 (MQ=255)
                                   ctccGGCAGTGGTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                     <  4:263827/139‑1 (MQ=255)
                                    tccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCt                                                                                    >  5:139300/1‑139 (MQ=255)
                                      cGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGa                                                                                  >  4:92246/1‑139 (MQ=255)
                                           gtgtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                             <  3:348836/139‑1 (MQ=255)
                                           gtgtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                             <  4:6852/139‑1 (MQ=255)
                                                        ttGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTaat                                                                >  6:183995/1‑138 (MQ=255)
                                                               aaCTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCACGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAt                                                         >  8:200576/1‑139 (MQ=255)
                                                                 cTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAttg                                                       <  6:123569/139‑1 (MQ=255)
                                                                 cTTTTCATTCGCGTCACGCACGACAAAGATCGTTTCAACTTTATTCAACGCGATGAGATCATTTATCTTTTTTTTAAAAGCGATTCCCTGTCCCATCACGATTATTTCCTGATCATCCTCTTTTATTAAAGCCGCAttg                                                       <  4:137764/139‑1 (MQ=255)
                                                                            cgtcgcGCACGACAAAGATCTTTTCCACTTTATTAATAGGGATGAGATCATTTTTCTTTTTTTGAAAACCGATTCCCGGACCCATCACCATTTTTTCCTGAACATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATaa                                            >  7:299902/1‑138 (MQ=255)
                                                                                         aaaGATCTTTTCCAATTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTACTGATCATCCTCTTTTATTAAAGCCGCATTGTTTTTTAATACTTTATAGATTTTc                               <  8:60846/139‑1 (MQ=255)
                                                                                          aaGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCa                              <  8:22806/139‑1 (MQ=255)
                                                                                           aGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCaa                             <  4:176191/139‑1 (MQ=255)
                                                                                           aGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCaa                             <  1:86213/139‑1 (MQ=255)
                                                                                           aGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTATGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCaa                             <  5:232057/139‑1 (MQ=255)
                                                                                                ttttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAggt                        >  1:302419/1‑138 (MQ=255)
                                                                                                  ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                      >  2:15785/1‑139 (MQ=255)
                                                                                                  ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                      >  5:146440/1‑139 (MQ=255)
                                                                                                  ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                      >  1:164345/1‑139 (MQ=255)
                                                                                                  ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                      >  4:193212/1‑139 (MQ=255)
                                                                                                     cACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGATTAATACTTTATAGATTTTCAAGAGGTTAtct                   <  8:102371/139‑1 (MQ=255)
                                                                                                       cTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAtctct                 >  1:129167/1‑139 (MQ=255)
                                                                                                          tATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTccc              >  2:324611/1‑139 (MQ=255)
                                                                                                            atCATAGGGATCAGATCATTTTTCTTTTTTTGAAAACAGATTCCCGGTCCCATCACGATTTTTTACTGAGCAGCCTCTATTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTAAAGATGTTATCTCTCCCGc            >  7:269795/2‑139 (MQ=255)
                                                                                                             tCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGc            <  2:164345/138‑1 (MQ=255)
                                                                                                               aTAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCg             <  5:326163/135‑1 (MQ=255)
                                                                                                               aTAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCg             >  6:326163/1‑135 (MQ=255)
                                                                                                                      tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt  >  7:331871/1‑139 (MQ=255)
                                                                                                                      tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt  >  3:275601/1‑139 (MQ=255)
                                                                                                                          |                                                                                                                                      
TAGCTGATGATATCCTCAGCTATTTCAATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTAAACTTTTCATTCTCGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTT  >  CP006881/3724597‑3724853

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A