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
A27 F53 I1 R1 117 75.6 2693952 95.6% 2575418 126.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 3,723,915 C→T V243V (GTC→GTT)  U712_19195 → putative transporter ywcJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,723,9150CT98.3% 196.7 / NA 58V243V (GTC→GTT) U712_19195putative transporter ywcJ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (26/31);  minor base A (1/0);  total (27/31)
Fisher's exact test for biased strand distribution p-value = 4.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACAGCATTGCCAATATGTGCACATTCGCCATCTCACTTTTGATCGAGCACCCTGATACAGTGACAGTAATGGGAGCAGTCAGAAACTTAATTCCCGTTACACTCGGCAACCTGACCGCGGGAATGGTCATGATGGGCTGGATGTATTACACGCTCAATCCCGATAAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGTGATATAGC  >  CP006881/3723787‑3724042
                                                                                                                                |                                                                                                                               
cacaTCATTGCCAATATGTGCACATTCGCCATCTCGCTCTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCt                                                                                                                       <  6:185028/139‑1 (MQ=255)
  caGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                     <  8:245491/139‑1 (MQ=255)
  caGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                     <  3:334412/139‑1 (MQ=255)
  caGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                     <  1:227006/139‑1 (MQ=255)
  caGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                     <  8:129985/139‑1 (MQ=255)
   aGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGa                                                                                                                    >  1:283444/1‑139 (MQ=255)
   aGCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTAATGATGGGCTGGa                                                                                                                    >  1:3298/1‑139 (MQ=255)
    gCATTGCCAATATGTGCACATTCGCGATCTCGCTTTTGATCGAGCACCCTGATAGAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATCGTTATGATGGGCTGGAt                                                                                                                   <  3:231707/139‑1 (MQ=255)
    gCATTGCCAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGAt                                                                                                                   <  5:188121/139‑1 (MQ=255)
          ccAATATGTGCACATTCGCCATCTCGCTTATGATCGAGCACCCTGATACAGTGACACTGATCGCAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATAGGCTGGATgaacta                                                                                                             >  4:112485/1‑134 (MQ=255)
           cAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGtactac                                                                                                            <  1:87708/139‑1 (MQ=255)
           cAATATGTGCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGtactac                                                                                                            <  2:48482/139‑1 (MQ=255)
                tgtgCACATTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACt                                                                                                       <  3:278403/139‑1 (MQ=255)
                 gtgCAGATTCGCGATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGATACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGTATAGTTATGATGGGCTGGATGTACTACACACt                                                                                                       <  3:112485/138‑1 (MQ=255)
                    cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAAt                                                                                                   >  8:212227/1‑139 (MQ=255)
                    cacaTTCGCCATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAAt                                                                                                   >  1:225915/1‑139 (MQ=255)
                            ccATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCt                                                                                                                       >  1:86414/1‑111 (MQ=255)
                            ccATCTCGCTTTTGATCGAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCt                                                                                                                       <  2:86414/111‑1 (MQ=255)
                                             gAGCACCCTGATACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCa                                                                            <  2:225915/137‑1 (MQ=255)
                                                    attaTACAGTTAAACTGATGGGAGAAGACTTAAAGTTAATCCCGGTTACGCTCTGCAATCTGACCGCGGGAATATTTATGTTGGGCTGGAGGTACTAAACAGTTAATCCTGTTCAATAAAAAAACTTCCAGAGATCACt                                                                   <  6:230799/136‑1 (MQ=255)
                                                       aTACAGTGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTccc                                                                >  4:284232/1‑139 (MQ=255)
                                                         aCAGTGACACTGATGGTAGCAGTCAGAAAATTAATCCCGGTTACGCTGGGCAAGCTGACGGCGGTAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTTATCAATAAAAAAACTTCCAGAGATCACTCCCTg                                                              <  6:21423/139‑1 (MQ=255)
                                                             tGACACTTATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGCCAATCTGCCCGCGGGAAGAGTTTGTATGGTCTGGATGTACTACACCCTGAATCCTGATCAATAAAAAACCTTCCAGAGATCACTCCCTGAAAg                                                          >  6:44598/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCGCGTTACGCTCGGCAATCTGACAGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCTAg                                                          >  8:153093/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATggg                                                                                                                         >  2:323752/1‑76 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATggg                                                                                                                         <  1:323752/76‑1 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                     >  8:20839/1‑80 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTgg                                                                                                                     <  7:20839/80‑1 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACt                                                                                                       <  1:232199/94‑1 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACt                                                                                                       >  2:232199/1‑94 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                          >  1:90842/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                          >  5:284841/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                          >  5:21423/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                          >  4:159420/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                          >  8:17682/1‑139 (MQ=255)
                                                             tGACACTGATGGGAGCAGTCAGAAACATAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAg                                                          >  5:230799/1‑139 (MQ=255)
                                                               acactgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGt                                                         >  8:233630/7‑138 (MQ=255)
                                                                 cctgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGCCCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTTAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCaa                                                      <  1:211762/135‑1 (MQ=255)
                                                                 actgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCa                                                                     >  4:89479/5‑124 (MQ=255)
                                                                 actgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCa                                                                     <  3:89479/120‑1 (MQ=255)
                                                                 actgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCaa                                                      <  3:159420/135‑1 (MQ=255)
                                                                 actgaTGGGAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCa                                                       >  2:245913/5‑138 (MQ=255)
                                                                        ggAGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGt                                                <  1:245913/138‑1 (MQ=255)
                                                                          aGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTa                                                                                                             <  7:118866/75‑1 (MQ=255)
                                                                          aGCAGTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTa                                                                                                             >  8:118866/1‑75 (MQ=255)
                                                                              gTCAGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCg                                         <  6:284841/139‑1 (MQ=255)
                                                                                 aGAAACTTAATCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCga                                        >  5:295551/1‑137 (MQ=255)
                                                                                         aaTCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCa                                                                            <  6:117957/93‑1 (MQ=255)
                                                                                         aaTCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTg                               >  7:192262/1‑138 (MQ=255)
                                                                                         aaTCCCCGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTg                               >  1:115879/1‑138 (MQ=255)
                                                                                          atccccGTTACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGa                              <  7:17682/135‑1 (MQ=255)
                                                                                               cGTTACGCTCGGCAATCTGACAGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGc                        >  5:89295/1‑139 (MQ=255)
                                                                                                 ttACGCTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTg                      >  3:249740/1‑139 (MQ=255)
                                                                                                     gcTCGGCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACa                  <  7:233630/138‑1 (MQ=255)
                                                                                                         ggCAATCTGACCGCGGGAATAGTTAGGATGGGCTGGATGTACTACACACTGAATCCTGAGCAAAAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATg                <  7:52939/137‑1 (MQ=255)
                                                                                                          gCAATCTGACCGCGGGAATAGTTATGATGGGCTGGATGTACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAg             <  7:212227/139‑1 (MQ=255)
                                                                                                          gCAAGCTGCCCGCGGTAATAGTTATGATGGGCTGGATGAACTACACACTGAATCCTGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAg             <  3:99462/139‑1 (MQ=255)
                                                                                                                     gcgGTAATAGTTAGGAGGGGCTGGATGTACTACACACTGAATCCGGATCAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGTGATATAGc  <  4:249740/139‑1 (MQ=255)
                                                                                                                                |                                                                                                                               
CACAGCATTGCCAATATGTGCACATTCGCCATCTCACTTTTGATCGAGCACCCTGATACAGTGACAGTAATGGGAGCAGTCAGAAACTTAATTCCCGTTACACTCGGCAACCTGACCGCGGGAATGGTCATGATGGGCTGGATGTATTACACGCTCAATCCCGATAAATAAAAAAACTTCCAGAGATCACTCCCTGCAAGTCAAAGCGGTTATTCCGAGAGATCTTGAAGACGCTGGACATGCAGCGTGATATAGC  >  CP006881/3723787‑3724042

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