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 3,724,849 A→T 100% intergenic (‑23/+17) U712_19200 ← / ← U712_19205 SacPA operon antiterminator/Uncharacterized protein ywcI

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,724,8490AT99.9% 180.6 / ‑7.5 56intergenic (‑23/+17)U712_19200/U712_19205SacPA operon antiterminator/Uncharacterized protein ywcI
Reads supporting (aligned to +/- strand):  ref base A (1/0);  major base T (25/29);  minor base G (0/1);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTAT‑CTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCAGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCGCGGCGGCTTTCGCTTTTTGTTTTT  >  CP006881/3724715‑3724984
                                                                                                                                       |                                                                                                                                       
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                                                                                                                     <  6:139300/138‑1 (MQ=255)
                 ttttGAAAAGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTAc                                                                                                                     <  4:275601/138‑1 (MQ=255)
                        aaGCGATTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCtttt                                                                                                             <  3:110318/139‑1 (MQ=255)
                             aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                                        <  8:231949/139‑1 (MQ=255)
                             aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                                        <  6:146934/139‑1 (MQ=255)
                             aTTCCCGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                                        <  5:153500/139‑1 (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                                                                                                        <  2:248790/110‑1 (MQ=255)
                                                          atcatcCTCTTTTATTAAAGCCGCATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCg                                                                                                        >  1:248790/1‑110 (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                                                    <  6:146440/139‑1 (MQ=255)
                                                                                 cATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGc                                                    >  3:181944/1‑139 (MQ=255)
                                                                                 cATTGTTGTTTAATACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGc                                                    >  8:155547/1‑139 (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)
                                                                                           taatACTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCTCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACa                                           >  1:311721/4‑138 (MQ=255)
                                                                                                cTTTATAGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACAtcttct                                     >  1:5284/1‑139 (MQ=255)
                                                                                                   tataGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGcc                                                                                                      >  3:236639/1‑71 (MQ=255)
                                                                                                   tataGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGcc                                                                                                      <  4:236639/71‑1 (MQ=255)
                                                                                                   tataGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTTCAAACATCTTCtttt                                  >  6:328915/1‑139 (MQ=255)
                                                                                                   tataGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCa                                               <  4:83389/126‑1 (MQ=255)
                                                                                                   tataGATTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCa                                               >  3:83389/1‑126 (MQ=255)
                                                                                                        aTTTTCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATaat                             >  8:295033/1‑138 (MQ=255)
                                                                                                          tttCAAGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAgc                           >  7:266139/1‑139 (MQ=255)
                                                                                                              aaGAGGTTAT‑CTCTCCCGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCgcgg                       <  2:47710/139‑1 (MQ=255)
                                                                                                              aaGAGGGAAT‑CTCTCCCGCCAATTGGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGcgcg                        <  1:324611/138‑1 (MQ=255)
                                                                                                                             cccGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCGCGGCGGCTTTCGCtttc         >  5:81992/1‑138 (MQ=255)
                                                                                                                              ccGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGcccg                                                                                   <  7:323233/64‑3 (MQ=255)
                                                                                                                              ccGCCAATTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGcccg                                                                                   >  8:323233/1‑62 (MQ=255)
                                                                                                                                    aTTTGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCCGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCGCGGCGGCTTTCGCTTTCTGctttt  <  6:248601/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
TGAGGTCATTTTTCTTTTTTTGAAAAGCGATTCCTGGTCCCATCACGATTTTTTCCTGATCATCCTCTTTTATTAAAGCCGCATTGTTGTTTAGTACTTTATAGATTTTCAAGAGGCTAT‑CTCTCCCGCCAATTAGCTTTTGACTGGGATTTTACCTCCTTTTGACCGCCATGTAAAGATGCGGGCCAGCTCTCTCCTGCTTTGGCGATTCCTTGAAGGCTTGCAAACATCTTCTTTTATAAAGCGCGGCGGCTTTCGCTTTTTGTTTTT  >  CP006881/3724715‑3724984

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