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 293,984 A→G 40.8% G11G (GGT→GGC)  ybaX ← predicted aluminum resistance protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE293,9840AG40.8% 61.7 / 122.8 164G11G (GGT→GGC) ybaXpredicted aluminum resistance protein
Reads supporting (aligned to +/- strand):  ref base A (43/54);  new base G (33/34);  total (76/88)
Fisher's exact test for biased strand distribution p-value = 6.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.97e-01

Only 100 of 168 total aligned reads displayed.

ATGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTATGGT  >  minE/293930‑294051
                                                      |                                                                   
aTGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAacac                                                       >  1:1865764/1‑69 (MQ=255)
aTGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAacac                                                       >  1:2929091/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAacac                                                       >  1:1672001/1‑68 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAacac                                                       >  1:2500826/1‑68 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:105878/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:1573226/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:327132/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:592378/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:1764237/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:744004/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:244433/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:1848132/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:2536490/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:2972093/1‑69 (MQ=255)
 tGGACTTCATCATATTGTTGTAATGCCTGAACCAGACAGGTGGTGGAATCCTGGCCTCCACTGAAcaca                                                      >  1:3121238/1‑69 (MQ=255)
  ggACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAAcaca                                                      >  1:1228540/1‑68 (MQ=255)
  ggACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAAcaca                                                      >  1:1100380/1‑68 (MQ=255)
  ggACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAAcaca                                                      >  1:2172783/1‑68 (MQ=255)
  ggACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAAcaca                                                      >  1:3415989/1‑68 (MQ=255)
  ggACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAAcaca                                                      >  1:417021/1‑68 (MQ=255)
               ttgttgTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGtt                                         >  1:2277278/1‑68 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCAc                                            >  1:3314996/1‑57 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGa                                  >  1:395020/1‑67 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGAt                                 >  1:3359637/1‑68 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGAt                                 >  1:1753645/1‑68 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGAt                                 >  1:1950403/1‑68 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGAt                                 >  1:1642401/1‑68 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGAt                                 >  1:2398418/1‑68 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGAt                                 >  1:2799911/1‑68 (MQ=255)
                       aTGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGAt                                 >  1:1029585/1‑68 (MQ=255)
                         gCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATaa                               <  1:2108350/68‑1 (MQ=255)
                         gCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATaa                               <  1:1398631/68‑1 (MQ=255)
                         gCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATaa                               <  1:2882154/68‑1 (MQ=255)
                          ccTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATc                             <  1:3278538/69‑1 (MQ=255)
                          ccTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATc                             <  1:956643/69‑1 (MQ=255)
                                    aCAGGTGGTGTAATCCTGGCCTCCACTGGACACAACGACAGCACGTTTCAt                                     <  1:360622/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:3363172/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:843171/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:2707298/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:802631/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:76629/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:1224602/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:1285308/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:714622/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:140061/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:2245439/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:3131115/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:3148211/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:574291/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:49047/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:456901/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:2116223/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:445859/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:1673689/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:3351593/51‑1 (MQ=255)
                                    aCAGGTGGTGGAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:1894683/51‑1 (MQ=255)
                                        gtggtgGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAAt                >  1:3042836/1‑68 (MQ=255)
                                        gtggtgGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAAt                >  1:903041/1‑68 (MQ=255)
                                         tggtggAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAAt                >  1:1339044/1‑67 (MQ=255)
                                              gAATCCTGGCCTCCACTGAACACAACGACAGCACGTTTCAt                                     <  1:1007812/41‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:1470841/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:3376394/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:2851069/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:407343/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:1666900/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:1559409/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:2141916/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:1318706/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:103204/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:1021779/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:2345806/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:940534/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:3003757/68‑1 (MQ=255)
                                                aTCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        <  1:2690818/68‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:1320524/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:1720550/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:1508566/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:1830734/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:1833159/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               >  1:2045625/1‑60 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:2112405/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:2230234/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:2168586/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:3247722/60‑1 (MQ=255)
                                                 tCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATa               <  1:3212597/60‑1 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGa                                  <  1:2073690/39‑1 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGa                                  <  1:1508913/39‑1 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTAt     >  1:2197759/1‑68 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTAt     >  1:81919/1‑68 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTAt     >  1:1159512/1‑68 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTAt     >  1:3186474/1‑68 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTAt     >  1:510613/1‑68 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTAt     >  1:1533124/1‑68 (MQ=255)
                                                   cTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTAt     >  1:3314162/1‑68 (MQ=255)
                                                     gACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTATGGt  <  1:888102/69‑1 (MQ=255)
                                                     gACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTATGGt  <  1:1002751/69‑1 (MQ=255)
                                                     gACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTATGGt  <  1:1088112/69‑1 (MQ=255)
                                                     gACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTATGGt  <  1:1886762/69‑1 (MQ=255)
                                                      aCCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        >  1:439856/1‑62 (MQ=255)
                                                      aCCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGt        >  1:2359636/1‑62 (MQ=255)
                                                      |                                                                   
ATGGACTTCATCATATTGTTGTAATGCCTGCACCAGACAGGTGGTGGAATCCTGACCTCCACTGAACACAACGACAGCACGTTTCATAGATAATCCTGCTTGAACAATAAAAGCGTTATGGT  >  minE/293930‑294051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A