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 3,723,912 G→A 100% M242I (ATG→ATA)  U712_19195 → putative transporter ywcJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,723,9120GA100.0% 200.7 / ‑6.6 65M242I (ATG→ATA) U712_19195putative transporter ywcJ
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (34/30);  minor base T (1/0);  total (35/30)
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.

CACAGCATTGCCAATATGTGCACATTCGCCATCTCACTTTTGATCGAGCACCCTGATACAGTGACAGTAATGGGAGCAGTCAGAAACTTAATTCCCGTTACACTCGGCAACCTGACCGCGGGAATGGTCATGATGGGCTGGATGTATTACACGCTCAATCCCGATAAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGTGATATA  >  CP006881/3723787‑3724040
                                                                                                                             |                                                                                                                                
cacaGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCt                                                                                                                     <  7:271797/139‑1 (MQ=255)
    gCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGAt                                                                                                                 <  7:100582/139‑1 (MQ=255)
    gCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGAt                                                                                                                 <  6:103961/139‑1 (MQ=255)
           cAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGtactac                                                                                                          <  4:278203/139‑1 (MQ=255)
               atGTGCACATTCACCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTCACCGCGGGAATAGTTATGATGGGCTGCATGTCCTacacac                                                                                                      >  6:47876/1‑137 (MQ=255)
                tgtgCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGTAACTTAATCCCCGTTACTCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACt                                                                                                     <  5:204839/139‑1 (MQ=255)
                 gtgCACATTCACCATCTCGCTTTTGATCGAGCTCCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGTGAATAGTTATGATGGGCTGGATGTACTACACACt                                                                                                     <  5:47876/138‑1 (MQ=255)
                       aTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATcct                                                                                              >  8:304970/1‑138 (MQ=255)
                                ctcGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGatcaata                                                                                      >  3:331758/1‑138 (MQ=255)
                                   gcTTTTGATCGAGCACCCTGATACAGGGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATaaaaa                                                                                  <  6:180397/138‑1 (MQ=255)
                                       ttGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTACTCCCCGTTACGCTCGGCAATCTGACCGCGGTAATAGTTAAGATGGGCTGGATGTACTACACACTGAATCCTGATCaaaaaaaaaa                                                                                <  5:57040/137‑1 (MQ=255)
                                               gCACCCTGATACTGTGACAGTTATGGGAGCAGTCAGAAACTTAATCCCCGTTCCGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACAACACACTGAATCCTTATCAATAAAAACACTTCCAgaga                                                                      <  2:136112/139‑1 (MQ=255)
                                               gCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                   >  6:234432/1‑94 (MQ=255)
                                               gCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                   <  5:234432/94‑1 (MQ=255)
                                                     taaTACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTc                                                                >  4:337023/3‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGCCCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  7:240296/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTa                                                                                                              >  6:35848/1‑85 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTa                                                                                                              <  5:35848/85‑1 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  3:8986/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  8:36623/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  8:308485/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  2:84238/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  5:346570/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  7:62922/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  7:129322/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCAAGAGATCACTCCCTGCAAg                                                        >  8:55850/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAACCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                        >  1:197011/1‑139 (MQ=255)
                                                                 actgttGGGAGCAGTCAGAAAATTAATCCCGGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTTATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCaa                                                    <  4:331758/134‑1 (MQ=255)
                                                                 actgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCATTAAAAAAACTTCCAGAGATCCCTCCCTGCAAGTCa                                                     >  8:132104/5‑138 (MQ=255)
                                                                 actgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCaa                                                    <  5:120226/135‑1 (MQ=255)
                                                                 actgaTGGGAGCAGTCAGAAACTAAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCa                                                     >  2:325994/5‑138 (MQ=255)
                                                                     aTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCg                                                >  7:160320/1‑139 (MQ=255)
                                                                         gAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTatgatg                                                                                                                         <  3:245226/62‑1 (MQ=255)
                                                                         gAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTatgatg                                                                                                                         >  4:245226/1‑62 (MQ=255)
                                                                             aGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCTCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAAGAAAAAAACTTCCAGAGATCACTCCCTGCAAGACAAAGCGGTAATTcc                                        >  2:188196/1‑139 (MQ=255)
                                                                               tCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATTGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCgc                                      >  6:84440/1‑138 (MQ=255)
                                                                               tCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTa                                                                                                           <  6:18246/70‑1 (MQ=255)
                                                                               tCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTcc                                        >  8:241606/1‑137 (MQ=255)
                                                                               tCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTcc                                        >  6:27160/1‑137 (MQ=255)
                                                                               tCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTcc                                        >  6:5470/1‑137 (MQ=255)
                                                                               tCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTcc                                        >  5:59101/1‑137 (MQ=255)
                                                                                cAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAAAAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCgag                                     <  7:304970/139‑1 (MQ=255)
                                                                                  gAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGGGGTAATAGTTATTATGGGCTGGATCTACTACAAACTGAATCCTTATCAATAAAAACACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCgagag                                   <  6:218968/139‑1 (MQ=255)
                                                                                  gAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAACCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCgagag                                   <  2:197011/139‑1 (MQ=255)
                                                                                          atcccggTTACGCTCGGAAATCTGACCGCGGTATTATTTATTATGGGCTGGATGTAATAAACACTTAATCCTGATAAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGaa                           <  8:129322/133‑1 (MQ=255)
                                                                                             cccGTTACGCTCGGCAATCTGACCGCGGTAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGAc                        <  8:62922/139‑1 (MQ=255)
                                                                                             cccGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGAc                        >  4:110599/1‑139 (MQ=255)
                                                                                               cGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGc                      <  3:337023/139‑1 (MQ=255)
                                                                                               cGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGc                      <  7:308485/139‑1 (MQ=255)
                                                                                               cGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGc                      >  8:160012/1‑139 (MQ=255)
                                                                                                gTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCt                     >  5:132731/1‑139 (MQ=255)
                                                                                                 ttACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGTGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTg                    <  7:55850/139‑1 (MQ=255)
                                                                                                         ggCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCgagag                                   <  7:10531/116‑1 (MQ=255)
                                                                                                         ggCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCgagag                                   >  8:10531/1‑116 (MQ=255)
                                                                                                         ggCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATg              <  3:110599/137‑1 (MQ=255)
                                                                                                         ggCAATCTGACCGCGGGAATAGTTATGATGGGCAGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATg              >  8:105100/1‑137 (MQ=255)
                                                                                                          gCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAg           <  6:59101/139‑1 (MQ=255)
                                                                                                           cAATCTGACCGCGGGAATAGTTATGATGGGCTGGAGGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGc          <  7:241606/139‑1 (MQ=255)
                                                                                                            aatcTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTTATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCg         <  8:70656/136‑1 (MQ=255)
                                                                                                            aatcTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCg         <  8:160320/136‑1 (MQ=255)
                                                                                                              tcTGACCGCAGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTCATCAATAAAAAAACTTCAAGAGATCACTCACTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGt        >  8:106450/2‑138 (MQ=255)
                                                                                                                   ccGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACt                                                                 <  8:306059/76‑1 (MQ=255)
                                                                                                                   ccGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACt                                                                 >  7:306059/1‑76 (MQ=255)
                                                                                                                   ccGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGTGata    >  2:76385/1‑137 (MQ=255)
                                                                                                                   ccGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGTGAtata  >  2:63944/1‑139 (MQ=255)
                                                                                                                             |                                                                                                                                
CACAGCATTGCCAATATGTGCACATTCGCCATCTCACTTTTGATCGAGCACCCTGATACAGTGACAGTAATGGGAGCAGTCAGAAACTTAATTCCCGTTACACTCGGCAACCTGACCGCGGGAATGGTCATGATGGGCTGGATGTATTACACGCTCAATCCCGATAAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGTGATATA  >  CP006881/3723787‑3724040

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