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 2,556,078 T→C 26.8% L46L (CTA→CTG)  gpmI ← phosphoglycero mutase III, cofactor‑independent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,556,0780TC26.8% 148.5 / 55.5 134L46L (CTA→CTG) gpmIphosphoglycero mutase III, cofactor‑independent
Reads supporting (aligned to +/- strand):  ref base T (40/58);  new base C (7/29);  total (47/87)
Fisher's exact test for biased strand distribution p-value = 2.50e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 134 total aligned reads displayed.

GGCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCGGGGTTTTAG  >  minE/2556014‑2556127
                                                                |                                                 
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:1982304/69‑1 (MQ=255)
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:546546/69‑1 (MQ=255)
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:2571122/69‑1 (MQ=255)
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:2781869/69‑1 (MQ=255)
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:3412995/69‑1 (MQ=255)
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:2811691/69‑1 (MQ=255)
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:2922796/69‑1 (MQ=255)
ggCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:1484382/69‑1 (MQ=255)
 gCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:1020677/68‑1 (MQ=255)
 gCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAggg                                               <  1:3358985/68‑1 (MQ=255)
 gCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGt                                              >  1:3171554/1‑69 (MQ=255)
 gCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGt                                              >  1:2658587/1‑69 (MQ=255)
 gCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGt                                              >  1:1514013/1‑69 (MQ=255)
 gCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGt                                              >  1:3290956/1‑69 (MQ=255)
 gCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGt                                              >  1:439819/1‑69 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:949251/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:3185947/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:2921573/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:2834114/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:2821266/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:488810/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:498097/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:2234571/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:2052628/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:926513/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:1904969/67‑1 (MQ=255)
           gAGTTACCCATCTGACGGGCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGAc                                      <  1:1684523/67‑1 (MQ=255)
                aCCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTa                                             >  1:2170516/1‑55 (MQ=255)
                aCCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTgg                                >  1:1884393/1‑68 (MQ=255)
                aCCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTgg                                >  1:1382051/1‑68 (MQ=255)
                       tGACGGTCAGGGAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAg                         >  1:1240647/1‑68 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGTAAGCGTCGATTAGGGTATGCGGACGATTGGCCca                            >  1:2150933/1‑65 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACg                                     >  1:217991/1‑56 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCcaca                          >  1:357521/1‑67 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCca                            >  1:2908922/1‑65 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCca                            >  1:2798166/1‑65 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCca                            >  1:3229747/1‑65 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCca                            >  1:269218/1‑65 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCca                            >  1:3382383/1‑65 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCca                            >  1:2155364/1‑65 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAg                         >  1:2848839/1‑68 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAg                         >  1:1545932/1‑68 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAg                         >  1:2113321/1‑68 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAg                         >  1:2655701/1‑68 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTg                                 >  1:867632/1‑60 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCcaca                          >  1:1829709/1‑67 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAg                         >  1:1817891/1‑68 (MQ=255)
                       tGACGGTCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAg                         >  1:2414116/1‑68 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:69827/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:546337/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:32827/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:3315358/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:614162/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:411995/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1214367/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1451066/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:3075527/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1300081/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1291837/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:384119/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1624832/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1248115/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2860366/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1728870/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2803702/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:173103/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:885452/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2252390/69‑1 (MQ=255)
                             tCAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2338306/69‑1 (MQ=255)
                             gcAGGCAGACCGACTTCCAAACCGGAAGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:292557/68‑1 (MQ=255)
                              cAGGCAGACCGACTTCCAGACCGGAAGCGTCGTTTAggg                                               <  1:2620230/39‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1697359/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:456240/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:916566/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2002584/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2183383/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2433407/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:1806452/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2575398/63‑1 (MQ=255)
                                   aGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:724766/63‑1 (MQ=255)
                                    gACCGACTTCCAGACCGGAAGCGTCTATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2208505/62‑1 (MQ=255)
                                    gACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATcc                  <  1:2607488/62‑1 (MQ=255)
                                     tccGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTTGCCCACAGTGCATcc                  <  1:328185/60‑1 (MQ=255)
                                       cGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCgggg        >  1:2618778/1‑69 (MQ=255)
                                       cGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCgggg        >  1:2058765/1‑69 (MQ=255)
                                         aCTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCGGGGt       >  1:3057291/1‑68 (MQ=255)
                                         aCTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCGGGGt       >  1:3056333/1‑68 (MQ=255)
                                             ccAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCGGGGTTTTAg  >  1:1968837/1‑69 (MQ=255)
                                             ccAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCGGGGTTTTAg  >  1:1769063/1‑69 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:427457/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:39744/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:3392420/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:1326908/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:3310264/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:701520/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:1526636/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:2146148/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:1131900/43‑1 (MQ=255)
                                                      aaGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:1008052/43‑1 (MQ=255)
                                                      aaGCGTCGATCAGGGTATGCGGACGATTGGCCCACAGTGCATc                   <  1:1841486/43‑1 (MQ=255)
                                                                |                                                 
GGCCTACTTCGGAGTTACCCATCTGACGGTCAGGCAGACCGACTTCCAGACCGGAAGCGTCGATTAGGGTATGCGGACGATTGGCCCACAGTGCATCCATTACCGGGGTTTTAG  >  minE/2556014‑2556127

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