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 775,538 A→G 68.8% K387K (AAA→AAG)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE775,5380AG68.8% 111.7 / 57.1 118K387K (AAA→AAG) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base A (29/8);  new base G (62/19);  total (91/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

Only 100 of 126 total aligned reads displayed.

TGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGT  >  minE/775477‑775604
                                                             |                                                                  
tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAACCCGTaa                                                             >  1:2680222/1‑69 (MQ=255)
tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                             >  1:772292/1‑69 (MQ=255)
tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                             >  1:1201333/1‑69 (MQ=255)
tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                             >  1:288849/1‑69 (MQ=255)
tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                             >  1:2454129/1‑69 (MQ=255)
tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                             >  1:2335969/1‑69 (MQ=255)
     tGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAt                                                        <  1:963609/69‑1 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:2585782/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:992935/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:632127/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:579090/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:3241630/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:2530065/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:2273056/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:2266607/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:1531874/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCGAAGACCGTAACCTATg                                                       >  1:151717/1‑69 (MQ=255)
      ggACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATAAATGCGAAGACCGTAACCTATg                                                       >  1:3417884/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAGTCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:1396900/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACg                                             >  1:2346191/1‑68 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:360874/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:3427716/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:2132907/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:3228760/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:1397277/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:2963093/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:2425631/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:1111701/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:1388905/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:132555/1‑69 (MQ=255)
                 gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAGACCGTAACCTATGACTTCGAACGt                                            >  1:905341/1‑69 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACTGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                          >  1:2001127/1‑69 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                          >  1:2992324/1‑69 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                          >  1:103650/1‑69 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                          >  1:2089885/1‑69 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                           <  1:413514/68‑1 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                           <  1:215109/68‑1 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                           <  1:1288346/68‑1 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                           <  1:1002253/68‑1 (MQ=255)
                                   ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                           <  1:66876/68‑1 (MQ=255)
                                         gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                           <  1:251616/62‑1 (MQ=255)
                                         gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                     >  1:2774260/1‑68 (MQ=255)
                                         gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                     >  1:432009/1‑68 (MQ=255)
                                              cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAt                >  1:166868/1‑68 (MQ=255)
                                              cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg               >  1:2528833/1‑69 (MQ=255)
                                              cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg               >  1:1975014/1‑69 (MQ=255)
                                               gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg               >  1:1159998/1‑68 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACTTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:817912/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:617799/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:293957/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:2885405/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:571311/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:2879782/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:2786476/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:3222826/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:1428818/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:1749670/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:1856523/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:2482237/1‑69 (MQ=255)
                                                   tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag          >  1:1431610/1‑69 (MQ=255)
                                                   tCAACCCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTa                            >  1:418862/1‑51 (MQ=255)
                                                    cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga         >  1:157687/1‑69 (MQ=255)
                                                    cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga         >  1:663349/1‑69 (MQ=255)
                                                    cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga         >  1:2289865/1‑69 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:328662/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:649822/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:2021907/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:412918/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:2167968/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:2178148/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:3386772/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:3299891/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:2662660/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:307168/66‑1 (MQ=255)
                                                     aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:2333005/66‑1 (MQ=255)
                                                     aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag        >  1:3304954/1‑69 (MQ=255)
                                                     aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag        >  1:1719292/1‑69 (MQ=255)
                                                     aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag        >  1:1683526/1‑69 (MQ=255)
                                                      atgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:2992589/66‑1 (MQ=255)
                                                      atgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag        <  1:2895741/66‑1 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTaa                           >  1:715857/1‑48 (MQ=38)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAAGTGCTGAAATGTTCAGAGtt      >  1:1091785/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:1165290/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:349641/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:681535/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:1572673/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:458608/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:2202576/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:3202750/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:2330927/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:2468269/1‑69 (MQ=255)
                                                       cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt      >  1:2806041/1‑69 (MQ=255)
                                                           aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:1885426/69‑1 (MQ=255)
                                                           aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:462317/69‑1 (MQ=255)
                                                           aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:1934197/69‑1 (MQ=255)
                                                           aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:1202619/69‑1 (MQ=255)
                                                           aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:1287802/69‑1 (MQ=255)
                                                           aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:2858904/69‑1 (MQ=255)
                                                            aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:496910/68‑1 (MQ=255)
                                                            aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt  <  1:2671653/68‑1 (MQ=255)
                                                             |                                                                  
TGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGT  >  minE/775477‑775604

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