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
A20 F53 I0 R4 206 63.7 2487030 95.4% 2372626 127.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,724,749 T→C 100% P26P (CCA→CCG)  U712_19200 ← SacPA operon antiterminator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,724,7490TC100.0% 168.5 / NA 50P26P (CCA→CCG) U712_19200SacPA operon antiterminator
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/26);  total (24/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGCTATTTCAATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTAAACTTTTCATTCTCGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCG  >  CP006881/3724614‑3724882
                                                                                                                                       |                                                                                                                                     
aGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGt                                                                                                                                    >  1:33674/1‑139 (MQ=255)
aGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGt                                                                                                                                    >  1:38384/1‑139 (MQ=255)
aGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGt                                                                                                                                    <  2:38384/139‑1 (MQ=255)
aGCTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGt                                                                                                                                    <  2:33674/139‑1 (MQ=255)
  cTATTTCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTcc                                                                                                                                  >  5:253093/1‑139 (MQ=255)
     tttCTATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCAt                                                                                                                               >  1:96944/1‑139 (MQ=255)
        ctatatGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCa                                                                                                                             <  4:181170/136‑1 (MQ=255)
                tcctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGAttttt                                                                                                                     >  3:217238/1‑138 (MQ=255)
                  ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGCTTCCCGCTCCCATCACTCTTTTTTcc                                                                                                                  >  1:246375/1‑139 (MQ=255)
                  ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                                                  <  6:138192/139‑1 (MQ=255)
                  ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                                                  >  6:148056/1‑139 (MQ=255)
                  ctccGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                                                  >  8:176229/1‑139 (MQ=255)
                  cgccGGCAGTGTTTGCAGGATTTGTTTCAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGATATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTcc                                                                                                                  <  5:24065/137‑1 (MQ=255)
                     cGGCAGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTGTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCCTCACGCTTTTTTCCt                                                                                                                 >  6:122989/1‑137 (MQ=255)
                         aGTGTTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcat                                                                                                           <  4:217238/139‑1 (MQ=255)
                            gtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCct                                                                                                        >  7:211853/1‑139 (MQ=255)
                            gtTTGCAGGATTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCct                                                                                                        >  3:118658/1‑139 (MQ=255)
                               tgaaGGATTTGTTTGTACTTTTCATTCTCTTCGCGAACGACAAAGATCTTTTCCACTTTATTAATAGGGTTGTGATCTATTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCctct                                                                                                      <  2:246375/135‑1 (MQ=255)
                                     aTTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTttatt                                                                                                >  6:265640/1‑138 (MQ=255)
                                     aTTTGTTTGAACTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTttatt                                                                                                >  4:292873/1‑138 (MQ=255)
                                            tgaaCTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCg                                                                                         <  8:211853/136‑1 (MQ=255)
                                              aaCTTTTCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCAt                                                                                      <  3:32604/139‑1 (MQ=255)
                                                   ttCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                                                          >  3:182244/1‑114 (MQ=255)
                                                   ttCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGatcatc                                                                                                          <  4:182244/114‑1 (MQ=255)
                                                   ttCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTaa                                                                                              >  3:43853/1‑126 (MQ=255)
                                                   ttCATTCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTaa                                                                                              <  4:43853/126‑1 (MQ=255)
                                                       ttCTCGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTa                                                                             <  6:253093/139‑1 (MQ=255)
                                                         ctcGTCGCGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTaa                                                                            <  5:148056/138‑2 (MQ=255)
                                                           cgtcgcGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATAc                                                                         >  7:208354/1‑139 (MQ=255)
                                                                   aCGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGa                                                                 <  7:176229/139‑1 (MQ=255)
                                                                     gACAAAGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGact                                                               <  1:28900/139‑3 (MQ=255)
                                                                          aGATCTTTTCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCaa                                                          <  1:65234/139‑1 (MQ=255)
                                                                               ttttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACATTATAGATTTTCAagagt                                                      >  3:172366/1‑137 (MQ=255)
                                                                                                aGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTTTTTAATACTTTATAGATTTTCaa                                                          <  4:209032/117‑1 (MQ=255)
                                                                                                aGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCaa                                                          >  3:209032/1‑117 (MQ=255)
                                                                                                     tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTTCCGCCAATTTGCtt                               >  7:102430/1‑139 (MQ=255)
                                                                                                     tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt                               >  6:75996/1‑139 (MQ=255)
                                                                                                     tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCtt                               >  8:33755/1‑139 (MQ=255)
                                                                                                          tCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTAGCTTTTGAc                          <  2:96944/139‑1 (MQ=255)
                                                                                                            aTTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACt                         <  5:174838/138‑1 (MQ=255)
                                                                                                            aTTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATACTCATTTTTTAACTCCGCATTTTTGGTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCTCAAATTTTCATTTGACTg                        >  6:202974/1‑139 (MQ=255)
                                                                                                             tttttCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTgg                       <  2:153007/139‑1 (MQ=255)
                                                                                                                 tCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGAtt                   >  5:134792/1‑139 (MQ=255)
                                                                                                                   tttttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGAtttt                 >  1:121784/1‑139 (MQ=255)
                                                                                                                      ttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTAc               <  7:89578/138‑1 (MQ=255)
                                                                                                                                cGATTCCCGGTACCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGAc    <  2:251001/139‑1 (MQ=255)
                                                                                                                                  aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg  <  4:118658/139‑1 (MQ=255)
                                                                                                                                  aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg  <  3:292873/139‑1 (MQ=255)
                                                                                                                                  aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg  <  3:178105/139‑1 (MQ=255)
                                                                                                                                  aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTATCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg  <  8:208354/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                     
AGCTATTTCAATATGCTCCTCCGGCAGTGTTTGCAGGATTTGTTTAAACTTTTCATTCTCGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTATCTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCG  >  CP006881/3724614‑3724882

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A