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 1,884,138 A→T 35.8% D115E (GAT→GAA)  rumA ← 23S rRNA (uracil‑5)‑methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,884,1380AT35.8% 78.5 / 75.7 92D115E (GAT→GAA) rumA23S rRNA (uracil‑5)‑methyltransferase
Reads supporting (aligned to +/- strand):  ref base A (35/24);  new base T (20/13);  total (55/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AGTTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCACGCTGG  >  minE/1884074‑1884199
                                                                |                                                             
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:2736841/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:1440012/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:3340140/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:1801348/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:1916190/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:748581/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:2214374/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:2940086/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:2763544/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:1068538/69‑1 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:2131981/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:1983150/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:3103965/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:1870987/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:2763180/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:3324491/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:149737/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:1396066/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:934119/1‑69 (MQ=255)
agtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgt                                                           >  1:62779/1‑69 (MQ=255)
 gtTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:2002580/68‑1 (MQ=255)
  ttCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCTGCGATCACTTCAGAGACTTCgt                                                           <  1:1105190/67‑1 (MQ=255)
   tCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgtgt                                                         >  1:104222/1‑68 (MQ=255)
   tCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCgtgt                                                         >  1:148066/1‑68 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:2256833/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:2206805/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:2176334/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:1006742/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:1165153/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:651224/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:3225003/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:3337265/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:1754574/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:1632028/69‑1 (MQ=255)
                 gcgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:1502153/69‑1 (MQ=255)
                  cgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:1282954/68‑1 (MQ=255)
                  cgcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCg                                          <  1:2207349/68‑1 (MQ=255)
                   gcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAg                                        <  1:648447/69‑1 (MQ=255)
                   gcgACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAg                                        <  1:2565658/69‑1 (MQ=255)
                     gACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACTTCgt                                                           <  1:2884465/48‑1 (MQ=255)
                              aGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACttt                             <  1:895394/69‑1 (MQ=255)
                              aGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACttt                             <  1:2048087/69‑1 (MQ=255)
                              aGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACttt                             <  1:2267873/69‑1 (MQ=255)
                              aGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACttt                             <  1:3276895/69‑1 (MQ=255)
                                       gAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgct                    >  1:833333/1‑69 (MQ=255)
                                       gAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgc                     >  1:1119229/1‑68 (MQ=255)
                                        aaCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgctg                   >  1:3288065/1‑69 (MQ=255)
                                        aaCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgctg                   >  1:537751/1‑69 (MQ=255)
                                         aCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgctgc                  >  1:2797297/1‑69 (MQ=255)
                                         aCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgctgc                  >  1:3050310/1‑69 (MQ=255)
                                         aCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgctgc                  >  1:2401539/1‑69 (MQ=255)
                                         aCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCgctgc                  >  1:2579957/1‑69 (MQ=255)
                                         aCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGAGCCGCACTTTTGCTTCgctgc                  >  1:1046736/1‑69 (MQ=255)
                                         aCATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATAGGGCGAGTGCCGCACTTTTGCTTCgctgc                  >  1:2345750/1‑69 (MQ=255)
                                               gCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             <  1:1873323/68‑1 (MQ=255)
                                                 gATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATc          <  1:2460960/69‑1 (MQ=255)
                                                 gATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATc          <  1:2098342/69‑1 (MQ=255)
                                                 gATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATc          <  1:1973753/69‑1 (MQ=255)
                                                 gATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATc          <  1:3410412/69‑1 (MQ=255)
                                                    cACTTGAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:2985766/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:3318693/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:1449999/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:498094/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:110078/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:862796/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:1784317/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:1098385/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:2371981/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCAc       >  1:1927127/1‑69 (MQ=255)
                                                    cACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGAACTTTTGCTTCgc                     >  1:918441/1‑55 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCAc                                >  1:969451/1‑39 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:916400/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:2746864/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:801832/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:1122104/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:745678/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:1230177/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:959739/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:1232756/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:48338/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:367345/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:3359865/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:1639369/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:180343/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:1815199/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:314589/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:229853/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTaa             >  1:2403292/1‑58 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTa              >  1:376199/1‑57 (MQ=255)
                                                         cAGAGACTTCGTGTTTCATTAATCGGGCGAGTGCAGCACTTTTGCTTCGCTGCTGTaa             >  1:119667/1‑58 (MQ=255)
                                                         cAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACtttt                            >  1:3396934/1‑43 (MQ=255)
                                                         cAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCACGCTgg  >  1:2857824/1‑69 (MQ=255)
                                                                |                                                             
AGTTCAGACTTAAACGCGCGCGACGGCGATAGCCCCAGGGAACATCGGCGATCACTTCAGAGACATCGTGTTTCATTAATCGGGCGAGTGCCGCACTTTTGCTTCGCTGCTGTAAATCCACGCTGG  >  minE/1884074‑1884199

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