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 1,354,874 C→T 34.2% A249A (GCC→GCT)  yohM → membrane protein conferring nickel and cobalt resistance

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,354,8740CT34.2% 53.3 / 37.0 70A249A (GCC→GCT) yohMmembrane protein conferring nickel and cobalt resistance
Reads supporting (aligned to +/- strand):  ref base C (4/42);  new base T (10/14);  total (14/56)
Fisher's exact test for biased strand distribution p-value = 3.11e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

GGCGCAGCAATCAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATGGCT  >  minE/1354806‑1354932
                                                                    |                                                          
ggCGCAGCAATCAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGcc                                                            >  1:279633/1‑69 (MQ=255)
ggCGCAGCAATCAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGcc                                                            >  1:2751826/1‑69 (MQ=255)
ggCGCAGCAATCAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGcc                                                            >  1:1974833/1‑69 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAACCGCGCTCCCTAtttt                                                   >  1:1985281/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:2470521/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:978732/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:3433715/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:2909504/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:2767875/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:107184/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:232729/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAtttt                                                   >  1:1373825/1‑67 (MQ=255)
           cAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCTCCCTAttt                                                    >  1:770643/1‑66 (MQ=255)
                     cagGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGtt                                        <  1:2564107/68‑1 (MQ=255)
                     cagGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGtt                                        <  1:1559584/68‑1 (MQ=255)
                     cagGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGtt                                        <  1:1290513/68‑1 (MQ=255)
                     cagGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGtt                                        <  1:2904134/68‑1 (MQ=255)
                          cGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTg                                       >  1:1480197/1‑64 (MQ=255)
                          cGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTg                                       >  1:2336507/1‑64 (MQ=255)
                          cGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTg                                       >  1:458699/1‑64 (MQ=255)
                          cGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTg                                       >  1:945785/1‑64 (MQ=255)
                              aaaCGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:3155249/69‑1 (MQ=255)
                              aaaCGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:1415406/69‑1 (MQ=255)
                              aaaCGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:3187611/69‑1 (MQ=255)
                              aaaCGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:2947159/69‑1 (MQ=255)
                              aaaCGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:650004/69‑1 (MQ=255)
                              aaaCGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:1354547/69‑1 (MQ=255)
                              aaaCGCTGGAGCGGATTTAACACTCTAGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:1236229/69‑1 (MQ=255)
                              aaaCGCTGGAGCGGATTTAAAACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:2138376/69‑1 (MQ=255)
                               aaCGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTa                              <  1:790411/68‑1 (MQ=255)
                                        gCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGgtgtg                     <  1:2117651/68‑1 (MQ=255)
                                         cGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGta                   <  1:1077481/69‑1 (MQ=255)
                                         cGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGta                   <  1:1772231/69‑1 (MQ=255)
                                         cGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGta                   <  1:2902847/69‑1 (MQ=255)
                                         cGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAATCGGTGTGta                   <  1:2057827/69‑1 (MQ=255)
                                          ggATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGtt                                        <  1:2456702/47‑1 (MQ=255)
                                           gATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtata                 <  1:1354629/69‑1 (MQ=255)
                                           gATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtata                 <  1:1778860/69‑1 (MQ=255)
                                           gATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtata                 <  1:3265857/69‑1 (MQ=255)
                                           gATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtata                 <  1:1831376/69‑1 (MQ=255)
                                           gATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtata                 <  1:2974059/69‑1 (MQ=255)
                                           gATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtata                 <  1:1469410/69‑1 (MQ=255)
                                           gATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtata                 <  1:261529/69‑1 (MQ=255)
                                                   acTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTa         <  1:2063271/69‑1 (MQ=255)
                                                   acTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTa         <  1:2373099/69‑1 (MQ=255)
                                                   acTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTa         <  1:598045/69‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:3339876/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:2184296/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:1527148/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:379462/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:3390625/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:1254582/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:3164371/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:3149980/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:1227356/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:3131230/67‑1 (MQ=255)
                                                         gCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:293241/67‑1 (MQ=255)
                                                          cTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATg     <  1:670617/66‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:2065090/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:1889134/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:897169/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:887415/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:1632582/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:619398/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:2079619/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:2392796/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:2980177/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:1078301/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:3385593/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:3131414/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:2400555/68‑1 (MQ=255)
                                                           tAAACGCGCTCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTTGGTGTGTATATGGGCGTACATGGCt  <  1:2516145/68‑1 (MQ=255)
                                                                  gcCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGtatt                 <  1:2342409/46‑2 (MQ=255)
                                                                    |                                                          
GGCGCAGCAATCAGCGTTCAGCAGGTCGCAAAACGCTGGAGCGGATTTAACACTCTCGCTAAACGCGCCCCCTATTTTTCCAGTCTGTTGATTGGCTTAGTCGGTGTGTATATGGGCGTACATGGCT  >  minE/1354806‑1354932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A