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 2,562,245 G→A 41.7% G59G (GGC→GGT)  lldR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,562,2450GA41.7% 37.3 / 63.6 92G59G (GGC→GGT) lldRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base G (14/39);  new base A (30/8);  total (45/47)
Fisher's exact test for biased strand distribution p-value = 7.50e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTCATGACGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCA  >  minE/2562193‑2562312
                                                    |                                                                   
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:669461/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:34374/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:1779858/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:2295830/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:1607866/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:2467631/69‑1 (MQ=255)
 gtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:842119/68‑1 (MQ=255)
  tCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt                                                     <  1:1459519/67‑1 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGt                                                      <  1:1503534/61‑1 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAg                                              >  1:3135761/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACCCCTTCGCTTACCAGTTTCGCCAg                                              >  1:2657803/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCtt                                                                 >  1:1001617/1‑50 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTtcgct                                                             >  1:911853/1‑54 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCa                                               >  1:436689/1‑68 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCa                                               >  1:2210985/1‑68 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:278270/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:2815374/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:1592134/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:514834/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:3236630/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:1109741/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:1684566/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:967578/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:1869038/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:1958370/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:1909993/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:802202/1‑69 (MQ=255)
       aCGCCAGCGAATAAACGTCCCGCCGCCAAGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                              >  1:395311/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:1931601/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:3342586/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:1114674/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:1135316/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:1211911/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:662973/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:17662/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:1345581/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:2362737/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:1591865/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:480546/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:56595/1‑69 (MQ=255)
              cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                       >  1:2536618/1‑69 (MQ=255)
                    aaCGTCCCGCCGCCGCGTCGACTGATCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                  >  1:1012729/1‑68 (MQ=255)
                    aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                  >  1:784326/1‑68 (MQ=255)
                    aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                  >  1:477900/1‑68 (MQ=255)
                    aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                  >  1:2424141/1‑68 (MQ=255)
                    aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                  >  1:1640195/1‑68 (MQ=255)
                    aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                  >  1:1873545/1‑68 (MQ=255)
                    aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                  >  1:1879949/1‑68 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:1603699/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:835012/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:3383000/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:3350025/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:756462/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:1936547/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:3235681/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:322245/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:3213057/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:3181433/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:302000/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:2902873/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:2194821/68‑1 (MQ=255)
                      cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:852750/68‑1 (MQ=255)
                            gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                         <  1:837777/69‑1 (MQ=255)
                            gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                         <  1:401970/69‑1 (MQ=255)
                            gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                         <  1:993090/69‑1 (MQ=255)
                            gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                         <  1:1897085/69‑1 (MQ=255)
                            gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                         <  1:248944/69‑1 (MQ=255)
                             ccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGt                        <  1:44940/69‑1 (MQ=255)
                               gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa                      <  1:1005308/69‑1 (MQ=255)
                               gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa                      <  1:1600278/69‑1 (MQ=255)
                               gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa                      <  1:494467/69‑1 (MQ=255)
                                     tCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                <  1:1935041/53‑1 (MQ=255)
                                          tGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGt            >  1:898074/1‑68 (MQ=255)
                                          tGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGt            >  1:358390/1‑68 (MQ=255)
                                          tGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGt            >  1:257678/1‑68 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTTCGTGATACGCCGAGTTGCATCGcc   <  1:605982/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:530981/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:57735/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:2588515/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:2176598/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:1982562/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:2818188/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:469965/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:449362/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:1444214/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:1268446/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:445156/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:1048227/69‑1 (MQ=255)
                                                  aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc   <  1:2910078/69‑1 (MQ=255)
                                                   cGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCa  >  1:1930493/1‑69 (MQ=255)
                                                   cGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCa  >  1:1896919/1‑69 (MQ=255)
                                                   cGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCa  >  1:1039537/1‑69 (MQ=255)
                                                    |                                                                   
TGTCATGACGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCA  >  minE/2562193‑2562312

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