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 2,721,334 G→C 54.9% L83V (CTA→GTA) ‡ yhfK ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,721,3340GC54.9% 8.7 / 55.1 51L83V (CTA→GTA) ‡yhfKconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (20/3);  new base C (14/14);  total (34/17)
Fisher's exact test for biased strand distribution p-value = 7.28e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

GACGCCAAGTACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAT  >  minE/2721269‑2721402
                                                                 |                                                                    
gACGCCAAGTACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCtg                                                                   >  1:113147/1‑69 (MQ=255)
gACGCCAAGTACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCtg                                                                   >  1:240255/1‑69 (MQ=255)
gACGCCAAGTACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCtg                                                                   >  1:2224734/1‑69 (MQ=255)
gACGCCAAGTACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCtg                                                                   >  1:2137574/1‑69 (MQ=255)
 aCGCCAAGTACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCtgt                                                                  <  1:1257077/69‑1 (MQ=255)
         tACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCa                                                           <  1:218316/68‑1 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:931216/1‑69 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:1364474/1‑69 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:818271/1‑69 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:2726655/1‑69 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:3166770/1‑69 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:1634803/1‑69 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:263691/1‑69 (MQ=255)
           ccAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGc                                                        >  1:3353646/1‑69 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:1894116/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:2949960/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:1041790/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:2307544/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:3233153/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:2718088/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:3138316/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:2894284/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:612600/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:1846930/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:164596/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:1774813/69‑1 (MQ=255)
                 ttAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:152775/69‑1 (MQ=255)
                   aaTCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAgg                                                  <  1:2015292/67‑1 (MQ=255)
                       cGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCa                                             >  1:3374293/1‑68 (MQ=255)
                       cGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCa                                             >  1:409884/1‑68 (MQ=255)
                       cGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCa                                             >  1:1548599/1‑68 (MQ=255)
                       cGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCa                                             >  1:910196/1‑68 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCt                                                       >  1:350621/1‑51 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:3174887/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:155524/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:1387750/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:2609987/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:67188/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:2894738/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:3389072/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:3827/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:1662805/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:1218085/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:220833/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:1685294/1‑69 (MQ=255)
                              cAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGCACCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGa                                     >  1:565821/1‑69 (MQ=255)
                                     ggCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCa                              <  1:1901879/69‑1 (MQ=255)
                                                 tCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGt                  >  1:521745/1‑69 (MQ=255)
                                                 tCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGt                  >  1:692391/1‑69 (MQ=255)
                                                 tCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGt                  >  1:912595/1‑69 (MQ=255)
                                                 tCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGAGt                  >  1:255072/1‑69 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGAc                                    >  1:260933/1‑39 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:369306/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:982476/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:3136741/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:2927146/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:1506016/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:2275184/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:2518440/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACg       >  1:1314864/1‑68 (MQ=255)
                                                             agtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACAAATGATTAAGCGTTTGAAAAAACg       >  1:1289435/1‑68 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     <  1:1650177/69‑1 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:1900487/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:875199/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:245895/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:1495820/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:2510601/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:257974/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:2659971/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:947535/1‑69 (MQ=255)
                                                              gtagCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGtt     >  1:272042/1‑69 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGttt    >  1:3037230/1‑67 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:1519611/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:1249219/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:1795784/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:555329/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:2223877/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:428535/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:2503776/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:2507832/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:318512/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:2673017/69‑1 (MQ=255)
                                                                 gCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAt  <  1:2788359/69‑1 (MQ=255)
                                                                 |                                                                    
GACGCCAAGTACCAGCGTTAATCCGGTCAGCAAAAAGGGCAGGGGAACATCTTTTGCCAGTAGTAGCTGTGTCAGCAAGCTACAGGTGGCAAACAGCGACGCACCAATGATTAAGCGTTTGAAAAAACGTTTAT  >  minE/2721269‑2721402

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