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 3,724,808 G→A 100% L7L (CTA→TTA)  U712_19200 ← SacPA operon antiterminator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,724,8080GA100.0% 192.4 / NA 59L7L (CTA→TTA) U712_19200SacPA operon antiterminator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/32);  total (27/32)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTAT‑CTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCAGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAA  >  CP006881/3724673‑3724940
                                                                                                                                       |                                                                                                                                     
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                                                                                                              >  4:193212/1‑139 (MQ=255)
                      ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                                                                                                              >  1:164345/1‑139 (MQ=255)
                      ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                                                                                                              >  5:146440/1‑139 (MQ=255)
                      ttCCACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTa                                                                                                              >  2:15785/1‑139 (MQ=255)
                         cACTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGATTAATACTTTATAGATTTTCAAGAGGTTAt‑ct                                                                                                          <  8:102371/139‑1 (MQ=255)
                           cTTTATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAt‑ctct                                                                                                        >  1:129167/1‑139 (MQ=255)
                              tATTCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTccc                                                                                                     >  2:324611/1‑139 (MQ=255)
                                atCATAGGGATCAGATCATTTTTCTTTTTTTGAAAACAGATTCCCGGTCCCATCACGATTTTTTACTGAGCAGCCTCTATTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTAAAGATGTTAT‑CTCTCCCGc                                                                                                   >  7:269795/2‑139 (MQ=255)
                                 tCATAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGc                                                                                                   <  2:164345/138‑1 (MQ=255)
                                   aTAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCg                                                                                                    <  5:326163/135‑1 (MQ=255)
                                   aTAGGGATGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCg                                                                                                    >  6:326163/1‑135 (MQ=255)
                                          tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCtt                                                                                         >  7:331871/1‑139 (MQ=255)
                                          tGAGATCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCtt                                                                                         >  3:275601/1‑139 (MQ=255)
                                               tCATTTTTCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGAc                                                                                    >  3:64773/1‑139 (MQ=255)
                                                  tttttCTTTTTTTGAAAAGCGATGCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTgg                                                                                 <  8:294900/139‑1 (MQ=255)
                                                   ttttCTTTTTTTGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAACCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTgg                                                                                 >  5:344820/1‑138 (MQ=255)
                                                          tttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTAc                                                                         >  5:146934/1‑139 (MQ=255)
                                                           ttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTAc                                                                         <  4:275601/138‑1 (MQ=255)
                                                           ttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTAc                                                                         <  6:139300/138‑1 (MQ=255)
                                                                  aaGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCtttt                                                                 <  3:110318/139‑1 (MQ=255)
                                                                       aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                            <  5:153500/139‑1 (MQ=255)
                                                                       aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                            <  8:231949/139‑1 (MQ=255)
                                                                       aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                            <  6:146934/139‑1 (MQ=255)
                                                                          cccggTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAACCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGcc                                                          <  6:344820/135‑1 (MQ=255)
                                                                              gTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTa                                                     <  1:15785/139‑1 (MQ=255)
                                                                                       cGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCgg                                            >  6:195064/1‑139 (MQ=255)
                                                                                       cGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTGAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGAGCGCCATGTAAAGATGCgg                                            >  2:124682/1‑139 (MQ=255)
                                                                                         aTTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGc                                          <  8:331871/139‑1 (MQ=255)
                                                                                         aTTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTATATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACAGCCATGTAAAGATGCGGGc                                          <  4:133587/139‑1 (MQ=255)
                                                                                         aTTTTTTCCAGATCATACTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGATAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAACGATGCGGGc                                          <  6:217506/139‑1 (MQ=255)
                                                                                          ttttttCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGc                                          <  8:65058/138‑1 (MQ=255)
                                                                                               tCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGct                                     <  6:122128/138‑1 (MQ=255)
                                                                                               tCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGct                                     <  2:129167/138‑1 (MQ=255)
                                                                                                    atcatcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTCTAGATTTTCAAGAGGTTAT‑CTCTCCCGGCAATTTGCTTTTGACTGGCATTTTACCTCCTTTTGACCTCCATGTAAAGATGCGGGCCCGCtctctc                                <  8:298792/138‑1 (MQ=255)
                                                                                                    atcatcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                            >  1:248790/1‑110 (MQ=255)
                                                                                                    atcatcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                            <  2:248790/110‑1 (MQ=255)
                                                                                                    atcatcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCtctctc                                <  7:200576/138‑1 (MQ=255)
                                                                                                    atcatcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTcc                               >  5:248601/1‑139 (MQ=255)
                                                                                                              tttATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGct                                     <  1:136733/123‑1 (MQ=255)
                                                                                                              tttATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGct                                     >  2:136733/1‑123 (MQ=255)
                                                                                                                tattaAAGCCGCATTGATGTTTAAAACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCCTGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGa                    <  1:87425/138‑1 (MQ=255)
                                                                                                                 attaAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGAt                   >  7:170421/1‑138 (MQ=255)
                                                                                                                      aGCCGCATTGTTGTTTAATACTTTATAGAATTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCGATGTAAAGTTGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTg             <  8:299902/139‑1 (MQ=255)
                                                                                                                       gCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGCCTGGGATTTTCCATCCTTTAGACCGCCATGTAAAGATCCGGGCCCGCTCTCTCCTTCTTTGGCGATTCTTTg             >  7:153947/1‑138 (MQ=255)
                                                                                                                       gCCGCATTGTTGATTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACGTCCTTTTGACCGACATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTg             >  4:140215/1‑138 (MQ=255)
                                                                                                                           cATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGc        >  8:155547/1‑139 (MQ=255)
                                                                                                                           cATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGc        >  3:181944/1‑139 (MQ=255)
                                                                                                                           cATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGc        <  6:146440/139‑1 (MQ=255)
                                                                                                                                ttgttTAATACTTTATAGATTTTCAAGAGG‑TATGCTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACAGCCATGTAAATATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCa   <  2:137538/139‑1 (MQ=255)
                                                                                                                                  gttTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCaa  >  1:47710/1‑138 (MQ=255)
                                                                                                                                   tttAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATg                                               <  2:209718/92‑1 (MQ=255)
                                                                                                                                   tttAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATg                                               >  1:209718/1‑92 (MQ=255)
                                                                                                                                       |                                                                                                                                     
CGTCGTGCACGACAAAGATCTTTTCCACTTTATTCATAGGGATGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTAT‑CTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCAGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAA  >  CP006881/3724673‑3724940

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