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 312,408 G→A 32.0% S155S (TCC→TCT)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE312,4080GA32.0% 100.2 / 56.3 112S155S (TCC→TCT) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (44/32);  new base A (22/14);  total (66/46)
Fisher's exact test for biased strand distribution p-value = 8.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01

Only 100 of 116 total aligned reads displayed.

AACTGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGG  >  minE/312343‑312475
                                                                 |                                                                   
 acTGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGgaga                                                                 <  1:1021338/69‑1 (MQ=255)
 acTGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGgaga                                                                 <  1:3098469/69‑1 (MQ=255)
 acTGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGgaga                                                                 <  1:3108848/69‑1 (MQ=255)
 acTGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGgaga                                                                 <  1:666002/69‑1 (MQ=255)
   tgcaCATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:2097078/66‑1 (MQ=255)
   tGATCATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:3018692/69‑1 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGTCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:719516/69‑1 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGGATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:2952007/69‑1 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCgg                                                                    >  1:2451945/1‑64 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGga                                                                   >  1:271446/1‑65 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGga                                                                   >  1:1324545/1‑65 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGga                                                                   >  1:1041986/1‑65 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGga                                                                   >  1:2423894/1‑65 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGga                                                                   >  1:2067554/1‑65 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGga                                                                   >  1:356922/1‑65 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:3304806/69‑1 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:2049765/69‑1 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:1504999/69‑1 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:1671504/69‑1 (MQ=255)
   tGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:1923256/69‑1 (MQ=255)
   tGAACATCACACACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGga                                                                   >  1:894548/1‑65 (MQ=255)
    gAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:3349233/68‑1 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:2972250/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:1093744/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:1431821/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:2464795/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:1500599/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:2596620/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:1925894/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:2713298/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:2793990/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:557691/1‑67 (MQ=255)
              cACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:1795465/1‑67 (MQ=255)
              aaCGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGc                                                      >  1:3001318/2‑67 (MQ=255)
                         tACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCAt                                         >  1:1067052/1‑69 (MQ=255)
                         tACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCAt                                         >  1:1884684/1‑69 (MQ=255)
                           cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                       >  1:2907463/1‑69 (MQ=255)
                           cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                       >  1:2983938/1‑69 (MQ=255)
                           cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                       >  1:3241804/1‑69 (MQ=255)
                           cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCg                                       >  1:409328/1‑69 (MQ=255)
                               tGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGata                                                               <  1:3064333/41‑1 (MQ=255)
                                gATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGtt                                  >  1:3412142/1‑69 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:457795/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:3045190/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:2789809/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:1314023/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:1910809/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:3038233/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:833466/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:696878/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:740981/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:3353513/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCTGCCACGTAGTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGAt                               <  1:1458861/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               <  1:3241389/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               <  1:1163593/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               <  1:171000/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               <  1:1140732/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               <  1:3193320/69‑1 (MQ=255)
                                   ggCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGAGTTGAt                               <  1:1410/69‑1 (MQ=255)
                                    gCATCTTTCATATTGGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATa                              >  1:3076006/1‑69 (MQ=255)
                                    gCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               <  1:1721953/68‑1 (MQ=255)
                                      aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                            <  1:3137172/69‑1 (MQ=255)
                                      aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                            <  1:899255/69‑1 (MQ=255)
                                      aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                            <  1:1830927/69‑1 (MQ=255)
                                      aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                            <  1:1948759/69‑1 (MQ=255)
                                      aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                            <  1:2065203/69‑1 (MQ=255)
                                             atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                     >  1:2807042/1‑69 (MQ=255)
                                             atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                     >  1:1676559/1‑69 (MQ=255)
                                             atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                     >  1:1651513/1‑69 (MQ=255)
                                             atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                     >  1:1907548/1‑69 (MQ=255)
                                             atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                     >  1:306076/1‑69 (MQ=255)
                                             atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                     >  1:1299484/1‑69 (MQ=255)
                                             atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                     >  1:2631810/1‑69 (MQ=255)
                                                ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               >  1:1342920/1‑56 (MQ=255)
                                                ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               >  1:2523029/1‑56 (MQ=255)
                                                ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               >  1:2339105/1‑56 (MQ=255)
                                                ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                               >  1:151954/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTg                                 >  1:531880/1‑40 (MQ=38)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAAcccc                         >  1:3127668/1‑48 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:1028473/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:681247/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:694062/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:2827876/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:853114/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:703952/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:148316/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:761173/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:592852/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:503369/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:1863975/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:2079554/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:2103106/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:2214147/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:2396210/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:2532180/1‑56 (MQ=255)
                                                              gTCAGAGATATCCTCCTGCGTCATAGTGCCATCGGTGTTGATAACCCCGACAACCa                 >  1:2602958/1‑56 (MQ=255)
                                                              gTCAGAGATATACTCCTGCGTCATAGTGCCATCGGTGTTGATATCCCCGACAACCa                 >  1:280040/1‑56 (MQ=255)
                                                                 ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTgg  >  1:571350/1‑68 (MQ=255)
                                                                 ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTgg  >  1:842894/1‑68 (MQ=255)
                                                                 ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTgg  >  1:2621321/1‑68 (MQ=255)
                                                                 |                                                                   
AACTGAACATCACCCACGCCCGACGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGG  >  minE/312343‑312475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A