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 1,903,767 C→G 43.8% D719H (GAT→CAT)  ptr ← protease III

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,903,7670CG43.8% 34.6 / 112.9 105D719H (GAT→CAT) ptrprotease III
Reads supporting (aligned to +/- strand):  ref base C (32/27);  new base G (18/28);  total (50/55)
Fisher's exact test for biased strand distribution p-value = 1.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.89e-01

Only 100 of 105 total aligned reads displayed.

TACATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCT  >  minE/1903711‑1903822
                                                        |                                                       
tACATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgt                                             <  1:857100/69‑1 (MQ=255)
tACATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgt                                             <  1:579238/69‑1 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:1020702/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:2119782/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:283148/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:1997991/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:1811789/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:3111357/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:3158233/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:3210846/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:3212707/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:150966/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:3278782/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:1277904/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:1263864/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:814643/1‑69 (MQ=255)
 aCATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgtt                                            >  1:74278/1‑69 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgttgtt                                         <  1:503408/69‑1 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgttgtt                                         <  1:893412/69‑1 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgttgtt                                         <  1:2868010/69‑1 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgttgtt                                         <  1:1945849/69‑1 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgttgtt                                         <  1:1435605/69‑1 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgttgtt                                         <  1:706584/69‑1 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgttgtt                                         <  1:641915/69‑1 (MQ=255)
    tCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCgt                                             <  1:2502904/65‑1 (MQ=255)
      tttGTTTCGACACCACTCTGAACCATCAGCGGCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGc                                       >  1:2648969/1‑69 (MQ=255)
      tttGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGc                                       >  1:162574/1‑69 (MQ=255)
      tttGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGc                                       >  1:621461/1‑69 (MQ=255)
      tttGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGc                                       >  1:2610141/1‑69 (MQ=255)
      tttGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGc                                       >  1:2652860/1‑69 (MQ=255)
      tttGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGc                                       >  1:2287419/1‑69 (MQ=255)
      tttGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGc                                       >  1:2077638/1‑69 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:1291851/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:1510446/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:1244012/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:2318183/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:2676954/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:818013/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:2864256/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:1379535/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:1390836/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:2883086/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:817815/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:2969658/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:454149/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:1207372/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:165770/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATGGCGTGACAGCGTTGTTGCCTGGGc                                 >  1:480820/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGCGCCCAACAGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:2675214/1‑68 (MQ=255)
             cGACACCACTCTGAACCATCAGAGCCCAACTGTTTTTGCACATGGCGTGCCAGCGTTGTTGCCTGGGc                                 >  1:163112/1‑68 (MQ=255)
                  ccacTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGt                           <  1:743004/69‑1 (MQ=255)
                  ccacTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGt                           <  1:756395/69‑1 (MQ=255)
                  ccacTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGt                           <  1:891639/69‑1 (MQ=255)
                  ccacTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGt                           <  1:838679/69‑1 (MQ=255)
                       ctGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCAt                        <  1:888239/67‑1 (MQ=255)
                       ctGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCAt                        <  1:869469/67‑1 (MQ=255)
                       ctGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCAt                        <  1:1480844/67‑1 (MQ=255)
                       ctGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCAt                        <  1:1520888/67‑1 (MQ=255)
                       ctGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCAt                        <  1:1152227/67‑1 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:580311/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:118330/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:763441/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:3299854/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:3116299/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:114462/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:196605/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:1113674/1‑69 (MQ=255)
                        tGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGtt                     >  1:936871/1‑69 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:116970/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1129156/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:865959/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:783571/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:881464/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:928864/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1171578/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1184153/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:146769/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:3153177/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1003784/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:2696233/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:2697509/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:2791834/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:2017179/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:194792/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1777343/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1297009/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:3317577/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:3420632/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:3431897/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1350833/41‑1 (MQ=255)
                          aaCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:1318672/41‑1 (MQ=255)
                           aCCATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:2883451/40‑1 (MQ=255)
                             cATCAGCGCCCAACTGTTTTTGCACATGGCGTGCCAGc                                               <  1:2365583/38‑1 (MQ=255)
                              aTCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGAt               <  1:3311366/69‑1 (MQ=255)
                              aTCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGAt               <  1:1680177/69‑1 (MQ=255)
                              aTCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGAt               <  1:1877695/69‑1 (MQ=255)
                              aTCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGAt               <  1:408364/69‑1 (MQ=255)
                              aTCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGAt               <  1:1181067/69‑1 (MQ=255)
                              aTCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGAt               <  1:2287656/69‑1 (MQ=255)
                                           tGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAActct  >  1:1681576/1‑69 (MQ=255)
                                                        |                                                       
TACATCTTTGTTTCGACACCACTCTGAACCATCAGCGCCCAACTGTTTTTGCACATCGCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCT  >  minE/1903711‑1903822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A