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 2,600,955 C→T 50.0% A202A (GCC→GCT)  prlC → oligopeptidase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,600,9550CT50.0% ‑3.2 / 67.0 74A202A (GCC→GCT) prlColigopeptidase A
Reads supporting (aligned to +/- strand):  ref base C (7/30);  new base T (14/23);  total (21/53)
Fisher's exact test for biased strand distribution p-value = 1.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCGACGAAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGTAATGACC  >  minE/2600892‑2601021
                                                               |                                                                  
tACCGACGAAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGc                                                               <  1:2526362/69‑1 (MQ=255)
   cgacgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGa                                                             <  1:178047/68‑1 (MQ=255)
   cgacgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGa                                                             <  1:2466990/68‑1 (MQ=255)
   cgacgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGa                                                             <  1:1143943/68‑1 (MQ=255)
   cgacgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGa                                                             <  1:1299549/68‑1 (MQ=255)
   cgacgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGa                                                             <  1:575188/68‑1 (MQ=255)
   cgacgaAGCGGAGCTGGCGGGGATGCCAAAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGa                                                             <  1:2338991/68‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCCGGCTGAAGCGAAag                                                          <  1:3110570/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:702454/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:750549/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:2147981/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:1372836/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:420433/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:413203/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:835490/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:2502584/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:3365262/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:1671784/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:1696501/69‑1 (MQ=255)
     acgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAag                                                          <  1:3083944/69‑1 (MQ=255)
      cgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAaga                                                         <  1:784836/69‑1 (MQ=255)
      cgaAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAaga                                                         <  1:2153464/69‑1 (MQ=255)
         aGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGa                                                             <  1:1043828/62‑1 (MQ=255)
                 tGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGc                                                               <  1:1076975/52‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAATAGCTGGAAGGTTAtt                                           <  1:3419541/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:2966368/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:3401584/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:534688/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:982598/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:127533/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:1521804/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:1579656/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:171729/63‑1 (MQ=255)
                          tGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTAtt                                           <  1:1126391/63‑1 (MQ=255)
                           gCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGAc                                    >  1:711784/1‑69 (MQ=255)
                               gAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTg                                <  1:3094621/69‑1 (MQ=255)
                               gAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTg                                <  1:2851395/69‑1 (MQ=255)
                               gAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTg                                <  1:2985084/69‑1 (MQ=255)
                               gAAAGCGCCCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTg                                <  1:1456484/69‑1 (MQ=255)
                                 aaGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCt                                       <  1:1147190/60‑1 (MQ=255)
                                 aaGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCt                                       <  1:2615808/60‑1 (MQ=255)
                                 aaGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCt                                       <  1:1668948/60‑1 (MQ=255)
                                 aaGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCt                                       <  1:2899227/60‑1 (MQ=255)
                                 aaGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGa                              <  1:121631/69‑1 (MQ=255)
                                 aaGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGa                              <  1:1821413/69‑1 (MQ=255)
                                  aGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGat                             >  1:3174232/1‑69 (MQ=255)
                                          ggctgCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCt                                       <  1:945046/51‑1 (MQ=255)
                                             tgCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGa                              <  1:529470/57‑1 (MQ=255)
                                             tgCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTa                  >  1:2751866/1‑69 (MQ=255)
                                             tgCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTa                  >  1:2265974/1‑69 (MQ=255)
                                                    aaaGCCCATGCTGAAGCGAAAGAGCTGTAAGGTTATTTGCTGACGCTGGatat                           >  1:913600/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGGAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:3295633/1‑53 (MQ=38)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:2961165/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:606818/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:2452729/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:1300727/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:47620/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:1574165/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:791186/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:2761961/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:2925890/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:3071890/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGatat                           >  1:2978941/1‑53 (MQ=255)
                                                    aaaGCCCAGGCTGAAGCGAAAGAGCTGGAAGCTTATTTGCTGACGCTGGatat                           >  1:1242121/1‑53 (MQ=39)
                                                      aGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGt         <  1:892704/69‑1 (MQ=255)
                                                      aGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGt         <  1:1015579/69‑1 (MQ=255)
                                                      aGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGt         <  1:1612567/69‑1 (MQ=255)
                                                      aGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGt         <  1:1760761/69‑1 (MQ=255)
                                                      aGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGt         <  1:263890/69‑1 (MQ=255)
                                                      aGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGt         <  1:20234/69‑1 (MQ=255)
                                                         ccAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGt         <  1:964004/66‑1 (MQ=255)
                                                             gCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGTAATGAcc  >  1:518350/1‑69 (MQ=255)
                                                             gCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGTAATGAcc  >  1:1873821/1‑69 (MQ=255)
                                                             gCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGTAATGAcc  >  1:2349180/1‑69 (MQ=255)
                                                              ccGAAGCGAAAGAGCTGGAATGTTATTTGCTGACGCTGGATATCCCAATCTACTTGccttt         <  1:3376308/61‑4 (MQ=255)
                                                               |                                                                  
TACCGACGAAGCGGAGCTGGCGGGGATGCCAGAAAGCGCGCTGGCTGCGGCAAAAGCCCAGGCCGAAGCGAAAGAGCTGGAAGGTTATTTGCTGACGCTGGATATCCCAAGCTACTTGCCGGTAATGACC  >  minE/2600892‑2601021

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