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 977,140 T→G 35.9% K669Q (AAG→CAG)  dcp ← dipeptidyl carboxypeptidase II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE977,1400TG35.9% 58.4 / 79.8 92K669Q (AAG→CAG) dcpdipeptidyl carboxypeptidase II
Reads supporting (aligned to +/- strand):  ref base T (28/31);  new base G (20/13);  total (48/44)
Fisher's exact test for biased strand distribution p-value = 2.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

TATCTCAGGCCAGCCATTGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAGG  >  minE/977073‑977204
                                                                   |                                                                
tatCTCAGGCCAGCCATTGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTa                                                                 <  1:582138/69‑1 (MQ=255)
tatCTCAGGCCAGCCATTGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTa                                                                 <  1:1440134/69‑1 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:991024/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:2644237/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:2763823/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:3071915/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:2279783/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:2268136/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:3195469/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:2082143/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:2042010/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:3417143/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:419573/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:1808718/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:639483/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:707223/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:655324/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:838741/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:123151/4‑69 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAg                                                                >  1:2441352/4‑68 (MQ=255)
  atccAGGCCAGCCATTGGTGGTGTTTATACGTTCAAGCCACGACGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:3172878/4‑69 (MQ=255)
  atccAGGCCAGACATTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAgg                                                               >  1:498543/4‑69 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTTAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:2372042/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:1690549/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:2284191/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:985959/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:1179914/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:307273/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:3309619/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:2133516/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:1280886/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:249590/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:2782952/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:87416/69‑1 (MQ=255)
           agccaTTGGTGGTGTTTATACGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTGAGGTGCCTTAcc                                                      <  1:1873280/69‑1 (MQ=255)
                ttGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:1125326/69‑1 (MQ=255)
                ttGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:2907230/69‑1 (MQ=255)
                ttGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:2735423/69‑1 (MQ=255)
                ttGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:2203875/69‑1 (MQ=255)
                ttGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:2097734/69‑1 (MQ=255)
                ttGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:1233445/69‑1 (MQ=255)
                  ggtggtGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCAt                                               >  1:945376/1‑69 (MQ=255)
                  ggtggtGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCAt                                               >  1:2897498/1‑69 (MQ=255)
                  ggtggtGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCAt                                               >  1:402142/1‑69 (MQ=255)
                  ggtggtGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCAt                                               >  1:1078771/1‑69 (MQ=255)
                      gtgtTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTc                                           <  1:255846/69‑1 (MQ=255)
                      gtgtTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTc                                           <  1:827582/69‑1 (MQ=255)
                        gtTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGa                                         <  1:3203059/69‑1 (MQ=255)
                        gtTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGa                                         <  1:2110130/69‑1 (MQ=255)
                        gtTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGa                                         <  1:2008964/69‑1 (MQ=255)
                           tataTGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:1062428/58‑1 (MQ=255)
                           tataTGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:1620832/58‑1 (MQ=255)
                           tataTGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:1827515/58‑1 (MQ=255)
                           tataTGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGcc                                                 <  1:2420964/58‑1 (MQ=255)
                               tGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTc                                           <  1:764160/60‑1 (MQ=255)
                                            aTGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:1027148/69‑1 (MQ=255)
                                            aTGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:1143324/69‑1 (MQ=255)
                                            aTGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:1367119/69‑1 (MQ=255)
                                            aTGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:2535990/69‑1 (MQ=255)
                                            aTGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:1719122/69‑1 (MQ=255)
                                            aTGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:1998291/69‑1 (MQ=255)
                                            aTGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:3138966/69‑1 (MQ=255)
                                               ttGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:564161/66‑1 (MQ=255)
                                                   agcaTCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGtt               <  1:2702318/68‑1 (MQ=255)
                                                   agcaTCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGtt               <  1:654633/68‑1 (MQ=255)
                                                   agcaTCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGtt               <  1:2965904/68‑1 (MQ=255)
                                                   agcaTCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGtt               <  1:3080607/68‑1 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCt                       >  1:270003/1‑56 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:2527482/1‑69 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:1592520/1‑69 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:231097/1‑69 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:1948526/1‑69 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:254745/1‑69 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:1981662/1‑69 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:1170292/1‑69 (MQ=255)
                                                       tCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACctc          >  1:2177031/1‑69 (MQ=255)
                                                           cATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     <  1:2459108/54‑1 (MQ=255)
                                                            aTAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGaa     >  1:1304471/1‑69 (MQ=255)
                                                               aTCTTAGGTTCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTc                     >  1:2039787/1‑50 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGc                   >  1:83856/1‑52 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGaaa    >  1:2934772/1‑67 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:1403517/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:2694388/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:614690/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:784783/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:306348/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:2407664/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:462181/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:375173/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:3427661/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:2147738/1‑69 (MQ=255)
                                                               aTCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAgg  >  1:2232100/1‑69 (MQ=255)
                                                                   |                                                                
TATCTCAGGCCAGCCATTGGTGGTGTTTATATGTTCAAGCCACGATGTTGCAGCATCGGCATAATCTTAGGTGCCTTACCGCGCCATTGTCGATACAGGCGTTCCAGATCTTCGCTGTTACCTCTGGAAAGG  >  minE/977073‑977204

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