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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 312,429 G→A 43.0% T148T (ACC→ACT)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE312,4290GA43.0% 28.1 / 63.0 86T148T (ACC→ACT) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (30/19);  new base A (22/15);  total (52/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.17e-01

TACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAA  >  minE/312368‑312487
                                                             |                                                          
tACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCAt                                                     >  1:1067052/1‑69 (MQ=255)
tACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCAt                                                     >  1:1961009/1‑69 (MQ=255)
tACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCAt                                                     >  1:1884684/1‑69 (MQ=255)
tACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCAt                                                     >  1:1837586/1‑69 (MQ=255)
  cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                                   >  1:3241804/1‑69 (MQ=255)
  cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                                   >  1:2983938/1‑69 (MQ=255)
  cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                                   >  1:2907463/1‑69 (MQ=255)
  cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                                   >  1:409328/1‑69 (MQ=255)
       gATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGtt                                              >  1:3412142/1‑69 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:1458861/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:3038233/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:3353513/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:2789809/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:1258983/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:457795/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:3045190/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:696878/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:1910809/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:1314023/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:740981/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:833466/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:1163593/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:3193320/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:171000/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:3241389/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:1140732/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:1661474/69‑1 (MQ=255)
          ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGAGTTGAt                                           <  1:1410/69‑1 (MQ=255)
           gCATCTTTCATATTGGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATa                                          >  1:3076006/1‑69 (MQ=255)
           gCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:3101376/68‑1 (MQ=255)
           gCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:488762/68‑1 (MQ=255)
           gCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           <  1:1721953/68‑1 (MQ=255)
             aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                                        <  1:2065203/69‑1 (MQ=255)
             aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                                        <  1:3137172/69‑1 (MQ=255)
             aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                                        <  1:899255/69‑1 (MQ=255)
             aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                                        <  1:1948759/69‑1 (MQ=255)
             aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                                        <  1:1830927/69‑1 (MQ=255)
                    atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                 >  1:2807042/1‑69 (MQ=255)
                    atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                 >  1:2631810/1‑69 (MQ=255)
                    atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                 >  1:306076/1‑69 (MQ=255)
                    atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                 >  1:1651513/1‑69 (MQ=255)
                    atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                 >  1:1299484/1‑69 (MQ=255)
                    atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                 >  1:1676559/1‑69 (MQ=255)
                    atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                 >  1:1907548/1‑69 (MQ=255)
                       ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           >  1:2523029/1‑56 (MQ=255)
                       ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           >  1:151954/1‑56 (MQ=255)
                       ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           >  1:2339105/1‑56 (MQ=255)
                       ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           >  1:3304381/1‑56 (MQ=255)
                       ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                           >  1:1342920/1‑56 (MQ=255)
                              ccACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:2472068/49‑1 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTg                                             >  1:531880/1‑40 (MQ=38)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAAcccc                                     >  1:3127668/1‑48 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:943705/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:503369/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:592852/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:672265/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:681247/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:694062/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:703952/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:761173/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:853114/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:1028473/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:2827876/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:148316/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:1863975/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:2079554/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:2602958/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:2532180/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:2396210/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:2103106/1‑56 (MQ=255)
                                     gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                             >  1:2214147/1‑56 (MQ=255)
                                     gTCAGAGATATACTCCTGCGTCATAGTGCCATCGGTGTTGATATCCCCGACAACCa                             >  1:280040/1‑56 (MQ=255)
                                        ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTgg              >  1:571350/1‑68 (MQ=255)
                                        ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTgg              >  1:2621321/1‑68 (MQ=255)
                                        ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTgg              >  1:842894/1‑68 (MQ=255)
                                        agagaTATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                                           <  1:1605382/38‑1 (MQ=39)
                                              atCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGAttt       >  1:219550/1‑69 (MQ=255)
                                              atCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGAttt       >  1:2176147/1‑69 (MQ=255)
                                                 ctcctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTtctc    >  1:1991978/1‑69 (MQ=255)
                                                 ctcctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTtctc    >  1:2667636/1‑69 (MQ=255)
                                                 ctcctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTtctc    >  1:1515583/1‑69 (MQ=255)
                                                   cctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCaa  <  1:2226525/69‑1 (MQ=255)
                                                   cctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCaa  <  1:1864354/69‑1 (MQ=255)
                                                   cctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCaa  <  1:870546/69‑1 (MQ=255)
                                                   cctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCaa  <  1:1514689/69‑1 (MQ=255)
                                                   cctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCaa  <  1:3402809/69‑1 (MQ=255)
                                                             |                                                          
TACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAA  >  minE/312368‑312487

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A