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 2,137,316 A→G 49.2% D185D (GAT→GAC)  truB ← tRNA pseudouridine synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,137,3160AG49.2% ‑5.3 / 61.2 68D185D (GAT→GAC) truBtRNA pseudouridine synthase
Reads supporting (aligned to +/- strand):  ref base A (3/31);  new base G (17/16);  total (21/47)
Fisher's exact test for biased strand distribution p-value = 1.52e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

TTTACTTACCGCCAGACGGCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCTT  >  minE/2137250‑2137380
                                                                  |                                                                
tttACTTACCGCCAGACGGCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGtcatc                                                                >  1:1122222/1‑69 (MQ=255)
tttACTTACCGCCAGACGGCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGtcat                                                                 >  1:727160/1‑68 (MQ=255)
   acttacCGCCAGACGGCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGtcatca                                                               <  1:1596268/67‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:1031119/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:3381719/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:3233151/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:3135169/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:650198/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:709390/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:2561199/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:746069/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:839282/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:1852467/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:940054/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:1660680/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:1573370/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:1195247/63‑1 (MQ=255)
           ccAGACGACGCAAGTAAATAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:1215347/63‑1 (MQ=255)
              gACGGCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGa                                                  <  1:968483/69‑1 (MQ=255)
              gACGGCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGa                                                  <  1:2423797/69‑1 (MQ=255)
                 ggCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGatat                                               <  1:1082734/69‑1 (MQ=255)
                  gcgcAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGatat                                               <  1:1746818/68‑1 (MQ=255)
                  gcgcAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGatat                                               <  1:2261311/68‑1 (MQ=255)
                  gcgcAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGAtata                                              <  1:166751/69‑1 (MQ=255)
                  gcgcAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGAtata                                              <  1:2297205/69‑1 (MQ=255)
                  gcgcAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGAtata                                              <  1:2173170/69‑1 (MQ=255)
                   cgcAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGAtata                                              <  1:1760907/68‑1 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:1453502/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:3160136/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:3134899/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:355264/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:582229/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:2788442/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:1099491/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:658112/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:1876516/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:1292105/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:1886243/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:1338693/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:3308389/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:749617/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:194312/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTGCGGATATAAGTGCCTTTTg                                   >  1:1363783/1‑69 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAATGATAGTCCGGATATAAGTCCCtttt                                    >  1:611783/1‑68 (MQ=255)
                             tAACATGCGCGCCACAACCGAGTTTTTCGCCGAGATCCTCAATGATAGTGCGGATAAAAGTGCCTTTTg                                   >  1:3351491/1‑69 (MQ=255)
                                 aTGCGCGCCACAACCGAGTTTTTCGCCGAGATCGTCAatga                                                           <  1:3383302/41‑1 (MQ=19)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            >  1:991624/1‑69 (MQ=255)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            >  1:1065793/1‑69 (MQ=255)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            <  1:882267/69‑1 (MQ=255)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            <  1:793578/69‑1 (MQ=255)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            <  1:315293/69‑1 (MQ=255)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            <  1:1095463/69‑1 (MQ=255)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            <  1:2206041/69‑1 (MQ=255)
                                    cgcgcCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTg                            >  1:3088524/1‑69 (MQ=255)
                                           caGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTtcc                     <  1:2040328/69‑1 (MQ=255)
                                           caGCCGAGTTTTTCACCCAGGGCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTtcc                     <  1:2767693/69‑1 (MQ=255)
                                              ccGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTtccagc                  <  1:3264520/69‑1 (MQ=255)
                                              ccGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTtccagc                  <  1:890786/69‑1 (MQ=255)
                                                         aCCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCAt        <  1:188888/68‑1 (MQ=255)
                                                             aGGTCATCAATGATGGTGCGGTTATAAGTGCCTTTTGAGCAGTGTTTTtcc                     <  1:437214/51‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCTGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:2847361/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:2704888/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:2666655/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:2294807/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:2747634/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:860468/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:3075196/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:1700469/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:954193/69‑1 (MQ=255)
                                                              ggTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCtt  <  1:1597362/69‑1 (MQ=255)
                                                               gTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTtcc                     <  1:2369379/49‑1 (MQ=255)
                                                                  |                                                                
TTTACTTACCGCCAGACGGCGCAGGTAAATAACATGCGCGCCACAGCCGAGTTTTTCACCCAGGTCATCAATGATGGTGCGGATATAAGTGCCTTTTGAGCAGTGAATTTCCAGCTCCAGCTCATTGCCTT  >  minE/2137250‑2137380

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