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
A14 F1 I2 R1 70 59.9 2639336 94.5% 2494172 113.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,366,415 A→G Y163C (TAC→TGC)  arnB → uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,366,4150AG98.2% 198.2 / NA 54Y163C (TAC→TGC) arnBuridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (23/30);  minor base C (1/0);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACGCCACGCACTAAAGCCATCATTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTACAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGCCCGCCAGCTACGGATGC  >  NC_000913/2366280‑2366543
                                                                                                                                        |                                                                                                                                
ttACGCCACGCACTAAAGCCATCATTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCaa                                                                                                                               <  1:1078032/139‑1 (MQ=255)
ttACGCCACGCACTAAAGCCATCATTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCaa                                                                                                                               <  1:268974/139‑1 (MQ=255)
       aCGCACTAAAGCCATCATTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGa                                                                                                                        >  2:1111513/1‑139 (MQ=255)
                    atcatTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTACGGTATTGCAAAGGGCGACATATTGGCGCa                                                                                                            <  1:845506/139‑1 (MQ=255)
                     tcatTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCaaa                                                                                                          >  1:1304292/1‑139 (MQ=255)
                     tcatTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGCTAC‑GTATTGCAAAGGGCGACATATTGgcg                                                                                                              >  2:933786/1‑135 (MQ=255)
                     tcatTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGCTAC‑GTATTGCAAAGGGCGACATATTGgcg                                                                                                              <  1:933786/135‑1 (MQ=255)
                              tGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGc                                                                                                 >  2:1107535/1‑139 (MQ=255)
                                        cGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTtttca                                                                                       >  2:436431/1‑139 (MQ=255)
                                          gTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTtttcatt                                                                                     >  1:728164/1‑139 (MQ=255)
                                          gTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTtttcatt                                                                                     >  1:377177/1‑139 (MQ=255)
                                           tGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTtttcattt                                                                                    >  1:131191/1‑139 (MQ=255)
                                             cgcCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTtttcatttca                                                                                  <  1:1111513/139‑1 (MQ=255)
                                               ccAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATg                                                                                >  1:825071/1‑139 (MQ=255)
                                               ccAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATg                                                                                <  1:571144/139‑1 (MQ=255)
                                                    agATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCAtt                                                                           <  2:994659/139‑1 (MQ=255)
                                                            aCGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAatat                                                                   >  2:1021201/1‑139 (MQ=255)
                                                               ccATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTAc                                                                <  1:1092984/139‑1 (MQ=255)
                                                                cATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTAcc                                                               >  2:983668/1‑139 (MQ=255)
                                                                 aTTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTCTCGAAGATGCCGCCCATGGCGTCGGTAC‑GTATTCCTAAGGGCGACGTATTGGCGCAAGAGGCACAGATATTTTTGACGTTCATGCCGAAAAAAATAGTACCt                                                              >  1:680822/1‑139 (MQ=255)
                                                                  ttCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCtg                                                             >  1:132501/1‑139 (MQ=255)
                                                                     gcgcCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGc                                                          <  1:436431/139‑1 (MQ=255)
                                                                      cgcCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCt                                                         >  1:780690/1‑139 (MQ=255)
                                                                               cGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGc                                                <  1:1001553/139‑1 (MQ=255)
                                                                               cGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGc                                                <  2:470276/139‑1 (MQ=255)
                                                                               cGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGc                                                <  2:728164/139‑1 (MQ=255)
                                                                                 aaCGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCt                                              <  2:780690/139‑1 (MQ=255)
                                                                                            aTCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTg                                   <  2:377177/139‑1 (MQ=255)
                                                                                             tCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAatat                                                                   >  2:796529/1‑106 (MQ=255)
                                                                                             tCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAatat                                                                   <  1:796529/106‑1 (MQ=255)
                                                                                             tCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGa                                  <  1:1021201/139‑1 (MQ=255)
                                                                                              cGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGAt                                 <  1:849740/139‑1 (MQ=255)
                                                                                               gCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATa                                >  2:853053/1‑139 (MQ=255)
                                                                                                cAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGgcg                                                                                                              >  2:777475/1‑60 (MQ=255)
                                                                                                cAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGgcg                                                                                                              <  1:777475/60‑1 (MQ=255)
                                                                                                cAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGc                                                                                                 <  2:124649/73‑1 (MQ=255)
                                                                                                cAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGc                                                                                                 >  1:124649/1‑73 (MQ=255)
                                                                                                    tATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACGGATAATGaa                           >  2:1062401/1‑139 (MQ=255)
                                                                                                     aTCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAgg                                                    <  2:981417/113‑1 (MQ=255)
                                                                                                     aTCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAgg                                                    >  1:981417/1‑113 (MQ=255)
                                                                                                      tCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGaaaa                         <  2:731806/139‑1 (MQ=255)
                                                                                                             tgctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGcc                  <  2:1304292/139‑1 (MQ=255)
                                                                                                             tgctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGcc                  >  2:1077066/1‑139 (MQ=255)
                                                                                                              gctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGccc                 <  2:574942/139‑1 (MQ=255)
                                                                                                               ctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGgc                                                                                                               >  1:783222/1‑44 (MQ=255)
                                                                                                               ctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGgc                                                                                                               <  2:783222/44‑1 (MQ=255)
                                                                                                               ctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTa                                                                          >  1:1025129/1‑81 (MQ=255)
                                                                                                               ctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTa                                                                          <  2:1025129/81‑1 (MQ=255)
                                                                                                               ctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGCCCg                <  1:1062401/139‑1 (MQ=255)
                                                                                                               ctgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGCCCg                <  2:825071/139‑1 (MQ=255)
                                                                                                                tgcCCATGCCGTCGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGCCCGc               <  1:1077066/139‑1 (MQ=255)
                                                                                                                            cGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTAc                                                                <  2:658012/78‑1 (MQ=255)
                                                                                                                            cGGTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTAc                                                                >  1:658012/1‑78 (MQ=255)
                                                                                                                             ggTAC‑GTATTGCAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGCCCGCCAGCTACGGATGc  <  1:1107535/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                
TTACGCCACGCACTAAAGCCATCATTCCGGTGCATTATGCCGGTGCGCCAGCAGATATTGACGCCATTCGCGCCATTGGCGAACGTTACGGCATCGCAGTTATCGAAGATGCTGCCCATGCCGTCGGTAC‑GTATTACAAAGGGCGACATATTGGCGCAAAAGGTACCGCTATTTTTTCATTTCATGCCATTAAAAATATTACCTGTGCTGAAGGTGGCCTGATTGTAACTGATAATGAAAACCTTGCCCGCCAGCTACGGATGC  >  NC_000913/2366280‑2366543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A