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 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,523,040 T→C 31.3% K225K (AAA→AAG)  dinD ← DNA‑damage‑inducible protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,523,0400TC31.3% 67.2 / 44.3 54K225K (AAA→AAG) dinDDNA‑damage‑inducible protein
Reads supporting (aligned to +/- strand):  ref base T (18/19);  new base C (9/7);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 7.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

TCCGCCAAGTTCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAAGAGATTAGCCG  >  minE/2522971‑2523104
                                                                     |                                                                
tCCGCCAAGTTCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGtt                                                                 >  1:971193/1‑71 (MQ=255)
 ccGCCAAGTTCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGttt                                                                >  1:1068161/1‑71 (MQ=255)
 ccGCCAAGTTCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGtt                                                                 <  1:693157/70‑1 (MQ=255)
      aaGTTCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGaa                                                            <  1:508427/70‑1 (MQ=255)
       aGTTCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGAAtt                                                          <  1:994742/71‑1 (MQ=255)
         ttCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGAATTCa                                                        <  1:814585/71‑1 (MQ=255)
            cTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACg                                                      <  1:2131351/70‑1 (MQ=255)
                 tGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATcc                                                <  1:127659/71‑1 (MQ=255)
                   gTTTGCCTCACCTTGCGCCCGACGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGAATTCACGCCATccc                                               >  1:1153063/1‑70 (MQ=255)
                   gTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCg                                              >  1:101483/1‑71 (MQ=255)
                   gTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGGTTTGAATTCACGCCATccc                                               >  1:763562/1‑70 (MQ=255)
                      tGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCtt                                           >  1:1838577/1‑71 (MQ=255)
                           cACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGAATTCACGc                                                     >  1:1083837/1‑56 (MQ=255)
                            aCCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGttt                                     >  1:738492/1‑71 (MQ=255)
                            aCCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGttt                                     >  1:879689/1‑71 (MQ=255)
                            aCCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGttt                                     >  1:1790469/1‑71 (MQ=255)
                            aCCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGtt                                      <  1:1814557/70‑1 (MQ=255)
                            aCCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTAAGttt                                     >  1:2022320/1‑71 (MQ=255)
                             ccTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGtttt                                    <  1:1381657/71‑1 (MQ=255)
                              cTTGCGACCCACGTCAAAGTGTGTGGTTTTTGCTTGCTGCTTTGAATTCACGCCATCCCGCTTGa                                         <  1:550946/65‑1 (MQ=255)
                              cTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTGACGCCATCCCGCTTGAGttttt                                   <  1:1654124/71‑1 (MQ=255)
                              cTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGttttt                                   >  1:57239/1‑71 (MQ=255)
                              cTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGtttt                                    <  1:879971/70‑1 (MQ=255)
                                tGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGaa                                                            >  1:1932851/1‑44 (MQ=255)
                                tGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGAATTCACGCCATCCCGCTTGAGTTTttct                                 >  1:1843053/1‑71 (MQ=255)
                                tGCGACCCACATCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCa                                                   >  1:732297/1‑53 (MQ=255)
                                 gCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTttc                                  <  1:1777561/69‑1 (MQ=255)
                                  cGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGAATTCACGCCATCCCGCTTGAGTTTttcttc                               <  1:1509159/71‑1 (MQ=255)
                                       cACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGttt                          <  1:2036969/71‑1 (MQ=255)
                                        aCGTCAAAGTGTGTGGTGTTTGCTTGCTGCTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTg                         >  1:2132259/1‑71 (MQ=255)
                                         cGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGttttt                                   >  1:1848512/1‑60 (MQ=255)
                                          gTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTggg                       <  1:809009/71‑1 (MQ=255)
                                           tCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTg                             <  1:313741/64‑1 (MQ=255)
                                           tCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTggg                       <  1:94564/70‑1 (MQ=255)
                                            cAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTTAGtt                                      <  1:1058902/54‑1 (MQ=255)
                                                     tggtgTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGtt                           >  1:1159180/1‑56 (MQ=255)
                                                     tggtgTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGtt                           >  1:987474/1‑56 (MQ=255)
                                                       gtgtTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTttc                                  >  1:266959/1‑47 (MQ=255)
                                                       gtgtTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGaaa             >  1:2103454/1‑68 (MQ=255)
                                                       gtgtTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAaga           <  1:1141352/70‑1 (MQ=255)
                                                       gtgtTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAaga           <  1:1542925/70‑1 (MQ=255)
                                                       gtgtTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAaga           <  1:1223765/70‑1 (MQ=255)
                                                       gtgtTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAaga           <  1:1586996/70‑1 (MQ=255)
                                                        tgtTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTttcttc                               <  1:1416064/49‑1 (MQ=255)
                                                        tgtTTGCTTGCTGCTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAAgaga         <  1:1926416/71‑1 (MQ=255)
                                                          tttGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGa                                         >  1:584722/1‑37 (MQ=255)
                                                            tgcttgctGCTTTGAATTCACGCCATCCCGCTTGAGt                                       >  1:1815705/1‑37 (MQ=255)
                                                            tgcttgctGCTTTGAATTCACGCCATCCCGCTTGAGt                                       >  1:1544772/1‑37 (MQ=255)
                                                            tgcttgctGCTTTGAATTCACGCCATCCCGCTTGAGt                                       >  1:251723/1‑37 (MQ=255)
                                                            tgcttgctGCTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAAGAGATTAg     >  1:882922/1‑71 (MQ=255)
                                                              cttgctGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAAGAGATTAgcc   <  1:1427205/71‑1 (MQ=255)
                                                               ttgctGCTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGa               <  1:1703914/58‑1 (MQ=255)
                                                                tgctGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTggg                       >  1:263300/1‑49 (MQ=255)
                                                                tgctGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTggg                       >  1:1166441/1‑49 (MQ=255)
                                                                 gctgctTTGAATTCACGCCATCCCGCTTGAGTTTTtcttct                              >  1:1969217/1‑41 (MQ=255)
                                                                 gctgctTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTg                             <  1:1022612/42‑1 (MQ=255)
                                                                 gctgctTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGaaa             >  1:1921320/1‑58 (MQ=255)
                                                                 gctGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAAGAGATTAgccg  >  1:1824024/1‑69 (MQ=255)
                                                                  ctGCTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTg                             <  1:24632/41‑1 (MQ=255)
                                                                   tGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAaga           >  1:335762/1‑58 (MQ=255)
                                                                     |                                                                
TCCGCCAAGTTCCTGAATGGTTTGCCTCACCTTGCGACCCACGTCAAAGTGTGTGGTGTTTGCTTGCTGTTTTGAATTCACGCCATCCCGCTTGAGTTTTTCTTCTGTTTGGGTAGCTCGAAAGAGATTAGCCG  >  minE/2522971‑2523104

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