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
A1 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,591,880 C→T 11.7% M201I (ATG→ATA)  yihF ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,591,8800CT11.7% 172.8 / 11.7 60M201I (ATG→ATA) yihFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (34/19);  new base T (2/5);  total (36/24)
Fisher's exact test for biased strand distribution p-value = 1.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.00e-01

TTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATGAAC  >  W3110S.gb/3591821‑3591944
                                                           |                                                                
ttcttttcttCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGAt                                                         <  1:3284461/69‑1 (MQ=255)
   ttttcttCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATaa                                                       <  1:1877443/68‑1 (MQ=255)
            aaTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAAc                                              <  1:364059/68‑1 (MQ=255)
            aaTCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAAc                                              <  1:67342/68‑1 (MQ=255)
                gcgcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAg                                                 <  1:3328689/61‑1 (MQ=255)
                gcgcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAg                                                 >  1:2409397/1‑61 (MQ=255)
                gcgcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAg                                                 >  1:51610/1‑61 (MQ=255)
                  gcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATc                                        <  1:2973485/68‑1 (MQ=255)
                  gcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATc                                        <  1:122400/68‑1 (MQ=255)
                  gcCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATc                                        <  1:292972/68‑1 (MQ=255)
                    cAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTc                                     <  1:763927/69‑1 (MQ=255)
                       agaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAAc                                              >  1:29967/1‑57 (MQ=255)
                       agaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAAc                                              >  1:3175686/1‑57 (MQ=255)
                       agaATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAAc                                              <  1:3186757/57‑1 (MQ=255)
                         aaTCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACtt                                >  1:2801290/1‑69 (MQ=255)
                         aaTCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACtt                                >  1:2363617/1‑69 (MQ=255)
                           tCAATGGTAAAACTTTTTGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTg                              >  1:254250/1‑69 (MQ=255)
                           tCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGaa                                               >  1:2169393/1‑52 (MQ=255)
                           tCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAAc                                              >  1:3470701/1‑53 (MQ=255)
                             aaTGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGAc                                  >  1:2162429/1‑63 (MQ=255)
                             aaTGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGAc                                  >  1:2114588/1‑63 (MQ=255)
                             aaTGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGcc                            >  1:3560563/1‑69 (MQ=255)
                               tGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGcc                            >  1:1268051/1‑67 (MQ=255)
                               tGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCt                           >  1:3680603/1‑68 (MQ=255)
                                ggTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGa                                                          >  1:1011195/1‑36 (MQ=255)
                                ggTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTc                         >  1:3356276/1‑69 (MQ=255)
                                ggTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTc                         >  1:1283512/1‑69 (MQ=255)
                                 gTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGAt                                                         >  1:2274920/1‑36 (MQ=255)
                                 gTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGAt                                                         >  1:357250/1‑36 (MQ=255)
                                 gTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGAt                                                         >  1:2597812/1‑36 (MQ=255)
                                 gTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACa                                             <  1:2037485/48‑1 (MQ=255)
                                    aaaCTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTc                                     >  1:3539368/1‑53 (MQ=255)
                                    aaaCTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTc                                     >  1:1136945/1‑53 (MQ=255)
                                    aaaCTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTc                                     >  1:2779883/1‑53 (MQ=255)
                                    aaaCTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAata                     >  1:2368881/1‑69 (MQ=255)
                                    aaaCTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAata                     >  1:1353461/1‑69 (MQ=255)
                                      aCTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAat                      <  1:2261122/66‑1 (MQ=255)
                                       cTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATcc                  >  1:1606067/1‑69 (MQ=255)
                                       cTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATc                   >  1:2334909/1‑68 (MQ=255)
                                         ttttGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATc                                        >  1:921854/1‑45 (MQ=255)
                                         ttttGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATc                                        >  1:2433514/1‑45 (MQ=255)
                                         ttttGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATc                                        >  1:3269034/1‑45 (MQ=255)
                                         ttttGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATc                                        >  1:3583234/1‑45 (MQ=255)
                                          tttGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCa                        <  1:2597290/60‑1 (MQ=255)
                                          tttGCCGTTACTTTGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCa                        <  1:3576415/60‑1 (MQ=255)
                                                gTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:3084798/69‑1 (MQ=255)
                                                  tACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:3236036/67‑1 (MQ=255)
                                                  tACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:1272806/67‑1 (MQ=255)
                                                   aCTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:1417461/66‑1 (MQ=255)
                                                   aCTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:758146/66‑1 (MQ=255)
                                                   aCTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGAc         <  1:1175330/66‑1 (MQ=255)
                                                   aCTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACaa       >  1:3508766/1‑68 (MQ=255)
                                                   aCTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACaa       >  1:2299690/1‑68 (MQ=255)
                                                     tttGTTCATTGGTGATTATTGCAGAACAATTTCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:640879/68‑1 (MQ=255)
                                                     tttGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:220881/68‑1 (MQ=255)
                                                     tttGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:1681603/68‑1 (MQ=255)
                                                     tttGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATg     <  1:3202597/68‑1 (MQ=255)
                                                      ttGTTTATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCa                        >  1:1697097/1‑48 (MQ=255)
                                                      ttGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATcc                  >  1:887831/1‑54 (MQ=255)
                                                       tGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATGAAc  >  1:2283555/1‑69 (MQ=255)
                                                           |                                                                
TTCTTTTCTTCTAATCGCGCCAGAGAATCAATGGTAAAACTTTTTGCCGTTACTTTGTTCATTGGTGATAATTGCAGAACAATATCTTCGACTTTGCCTTCAATATCCAGGTTAGACAATGAAC  >  W3110S.gb/3591821‑3591944

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