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
A18 F53 I0 R2 221 66.0 2680176 94.9% 2543487 126.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,723,652 C→T 100% L156L (CTG→TTG)  U712_19195 → putative transporter ywcJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,723,6520CT99.8% 189.3 / ‑7.3 58L156L (CTG→TTG) U712_19195putative transporter ywcJ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (30/26);  minor base A (2/0);  total (32/26)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
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.

AAGCTATGCCGGCAATTTGATCGGCGCCATTCTATTTGCCATTCTGATCAGCGCGACAGGGCTTTTTGAGGAGGCTTCTGTTCATTCCTTTTTGATTCATCTGGCAGAGCACAAAATGGAGCCGCCCGCTTCCGAACTGTTTTTCAGAGGGATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTTAAAGGGGAAGGGGCAAAGCTCTTTACCATGATGCTTTTCGTTTTCTGCTTCTTCATTTCCGGCTTCGAAC  >  CP006881/3723516‑3723787
                                                                                                                                        |                                                                                                                                       
aaGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTGCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTg                                                                                                                                       >  1:307770/1‑139 (MQ=255)
aaGCTAGCCCGGCAATTTACTCGGCGCCCTTCTGTTTGCCATCGTCACCCGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTg                                                                                                                                       <  3:202615/139‑1 (MQ=255)
      tGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGttttt                                                                                                                                  <  3:266781/138‑1 (MQ=255)
      tGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTACGAAATGttttt                                                                                                                                  >  5:34478/1‑138 (MQ=255)
      tGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCGGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATTGAGCCCCCCGCGTCCCAATTGttttt                                                                                                                                  >  4:178222/1‑138 (MQ=255)
       gacgccAATTAAATCGGCGCCATTCTGTTTGCCATCCGGATCCGCGCGACGGGACTTGTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCa                                                                                                                                <  6:176311/134‑1 (MQ=255)
       gCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGCCGGGACGTTTTGAGGAGCCGTCGGTTCATTCCTTTTTGATTGATTATGCAGAGCACAAAATGGCGCCGCCGGCTAGCGAATTGtgttt                                                                                                                                  >  2:172946/1‑137 (MQ=255)
               tttAATCGGCGCCATGCTGTTTGCAATCCTTATCTGCGCGACGGGACTTTTTGAGGAGCCTTATGTTCATTCCTTTTTGATTCATTTGGCAGAGCCCAAAATGTAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATg                                                                                                                        <  4:235008/139‑1 (MQ=255)
                   aTCGGCGCCATTCTGTTTGCAATCCTGATCAGCGCGAGGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGTCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCtg                                                                                                                     <  7:137308/138‑1 (MQ=255)
                                  tttGCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTtgtgt                                                                                                     >  5:298519/1‑139 (MQ=255)
                                  tttGCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTtgtgt                                                                                                     >  3:99512/1‑139 (MQ=255)
                                  tatGCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCACAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTtgt                                                                                                       <  5:236491/135‑1 (MQ=255)
                                     gCCATCCTTAGCAGCTCGACGGGACTTTTGGAGGAGCCTTCTGTTCATTACTTTTTGATTCATTTGGCAGAGAACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGcc                                                                                                  <  8:121373/139‑1 (MQ=255)
                                     gCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTg                                                                                                                                       <  7:181665/102‑1 (MQ=255)
                                     gCCATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTg                                                                                                                                       >  8:181665/1‑102 (MQ=255)
                                      ccATCCTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGcc                                                                                                  <  4:137446/138‑1 (MQ=255)
                                          ccTGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCCGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGcc                                                                                             >  2:57384/2‑139 (MQ=255)
                                            tGATCAGCGCGACGGGACTTTTTGAGGAGCCTTCTGTTAATTCCTTTTTGATTCATTTGGCAGATCACAAAATGGATCCGCCGGCTTACGAATTGTTTTTCAGAGGAATGCTGTTCAATTGGCTTGTGTGCGTCGCCtg                                                                                           >  2:228652/1‑138 (MQ=255)
                                                   cgcgACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGttttt                                                                                                                                  >  1:14280/1‑93 (MQ=255)
                                                   cgcgACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGttttt                                                                                                                                  <  2:14280/93‑1 (MQ=255)
                                                   cgcgACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCAtt                                                                                    >  7:33291/1‑139 (MQ=255)
                                                   cgcgACGGGACTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAAATGTTTTTCCGAGGAATGCAGTTCAAATTGCTTGCTTGCCACGCCTTTTTCAtt                                                                                    >  6:18422/1‑139 (MQ=255)
                                                        cgggacTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCATAGGAATGCTGTGCAATTGGCTTGTGTGACTCGCCTTTTTAATTCCAAt                                                                               >  8:60320/6‑139 (MQ=255)
                                                        cgggacTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCACAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAAt                                                                               <  8:117398/134‑1 (MQ=255)
                                                        cgggacTTTTTGAGGAGCCTTCTGTTCATTCCTGTTTGATTCATTTGGCAGAGCCCAAAATGGAGCCGCCGGCTTCCGACTTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTGCCTTCCAAt                                                                               >  8:2790/6‑139 (MQ=255)
                                                         gggacTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGTAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATg                                                                              <  7:243055/135‑1 (MQ=255)
                                                            acTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGtct                                                                           <  1:277978/138‑1 (MQ=255)
                                                             cTTTTTGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGtct                                                                           <  1:127951/138‑1 (MQ=255)
                                                                 ttGAGGAGCCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTctctca                                                                       <  4:54549/138‑3 (MQ=255)
                                                                     ggagcCTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAaaggg                                                                  >  2:214815/1‑139 (MQ=255)
                                                                       agccTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAaagggga                                                                <  3:283975/136‑1 (MQ=255)
                                                                       agccTTCTGTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAaagggga                                                                <  4:128188/136‑1 (MQ=255)
                                                                        gccTTCTGTTCATTCCTTTTTGATTAATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGATGTGCAATTGGATTGGGTTCCTAGCCTGTTTAATTCCAATGTATGTAAaagtggaa                                                               >  7:123395/3‑139 (MQ=255)
                                                                               gTTCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCa                                                         <  7:60320/138‑1 (MQ=255)
                                                                                ttCATTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCa                                                         <  3:176918/137‑1 (MQ=255)
                                                                                   aTTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGGTTCCGAATTGTTTTTCAGAGGAAAGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATCTCTCTCAAAGGGGAAGGAGCAAAGct                                                    >  3:104514/1‑139 (MQ=255)
                                                                                   aTTCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTAAGAGGAAAGCGGTGCAATTGGCGTGGGTGCCTCCCCTTTTTCATTCCCATGTCTCACAAAGTGGAAGGAGCaaacca                                                    >  4:191210/1‑136 (MQ=255)
                                                                                     tCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGcc                                                                                                  >  4:302290/1‑91 (MQ=255)
                                                                                     tCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGcc                                                                                                  <  3:302290/91‑1 (MQ=255)
                                                                                     tCCTTTTTGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGcttt                                                  >  6:55035/1‑137 (MQ=255)
                                                                                          tttGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCtttt                                                                                         >  7:85639/1‑95 (MQ=255)
                                                                                          tttGATTCATTTGGCAGAGCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCtttt                                                                                         <  8:85639/95‑1 (MQ=255)
                                                                                                           agCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGttt                             >  2:52603/1‑138 (MQ=255)
                                                                                                           agCACAAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTACAATGTCTCTAAAAGGGGAAGGAGCAAAGCTTTTTACCATTATGCTTTTAGtttt                            >  8:130228/1‑139 (MQ=255)
                                                                                                             cacaAAATGGAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCGCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCt                          >  1:219533/1‑139 (MQ=255)
                                                                                                             cacaAAATGGAGCCGCCGGCTTCCCAATAGTTTTTAAGAGGAATTCTGTTCAATTGGGATGTGTGCCTCGCCGTTTTAATTCCAATGTCTCTGAAAGGGGAATGAGCAAATCTTTTTACCAAGATTCTTTTGGttttga                          >  8:118570/1‑137 (MQ=255)
                                                                                                                     ggAGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGcttcttt                  >  5:159343/1‑138 (MQ=255)
                                                                                                                       aGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATTCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTGATTCCAATGTCTCTCAAAGGTGAAGGAGCAAAGCTTTTTAACATGATGCTGTTGGTTGTATTCTTCTTTAt                >  1:301317/1‑139 (MQ=255)
                                                                                                                       aGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTAt                >  7:312572/1‑139 (MQ=255)
                                                                                                                       aGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTAt                >  5:162071/1‑139 (MQ=255)
                                                                                                                       aGCCGCCGGCTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTATACCATCATGCTTTTCGTATTCTGCTTCTTTAt                >  6:84964/1‑139 (MQ=255)
                                                                                                                            ccggcTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGc                        >  7:303065/4‑126 (MQ=255)
                                                                                                                            ccggcTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGc                        <  8:303065/123‑1 (MQ=255)
                                                                                                                            ccggcTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCg           <  7:118570/136‑1 (MQ=255)
                                                                                                                            ccggcTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCg           >  5:238081/4‑139 (MQ=255)
                                                                                                                               gcTTCCGAATTGTTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCt        <  1:214815/139‑1 (MQ=255)
                                                                                                                                    cGAATTGTGTTTCAGAGGAATGCTGTGCAATTGGCGTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGaa   <  5:18422/139‑1 (MQ=255)
                                                                                                                                     gAATTGGTTTTCAGAGGAATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTCAAAGGGGAAGGAGCAAAGCTTTTTACCATGATGCTTTTCGTTTTCTGCTTCTTTATTTCCGGCTTTGAac  <  5:331511/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                       
AAGCTATGCCGGCAATTTGATCGGCGCCATTCTATTTGCCATTCTGATCAGCGCGACAGGGCTTTTTGAGGAGGCTTCTGTTCATTCCTTTTTGATTCATCTGGCAGAGCACAAAATGGAGCCGCCCGCTTCCGAACTGTTTTTCAGAGGGATGCTGTGCAATTGGCTTGTGTGCCTCGCCTTTTTCATTCCAATGTCTCTTAAAGGGGAAGGGGCAAAGCTCTTTACCATGATGCTTTTCGTTTTCTGCTTCTTCATTTCCGGCTTCGAAC  >  CP006881/3723516‑3723787

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