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 1,658,583 G→A 56.3% P261P (CCG→CCA)  ppx → exopolyphosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,658,5830GA56.3% 14.2 / 55.5 71P261P (CCG→CCA) ppxexopolyphosphatase
Reads supporting (aligned to +/- strand):  ref base G (15/16);  new base A (27/13);  total (42/29)
Fisher's exact test for biased strand distribution p-value = 1.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01

ACGTCTGGAAAAACTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATG  >  minE/1658520‑1658650
                                                               |                                                                   
aCGTCTGGAAAAACTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCt                                                                <  1:2151717/69‑1 (MQ=255)
aCGTCTGGAAAAACTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCt                                                                <  1:3332555/69‑1 (MQ=255)
aCGTCTGGAAAAACTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCt                                                                <  1:1522041/69‑1 (MQ=255)
   tCTGGAAAAACTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCttt                                                              >  1:1001639/1‑68 (MQ=255)
   tCTGGAAAAACTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCttt                                                              >  1:354735/1‑68 (MQ=255)
         aaaaCTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAaga                                                       >  1:1395264/1‑69 (MQ=255)
         aaaaCTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAag                                                        <  1:2632088/68‑1 (MQ=255)
         aaaaCTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAag                                                        <  1:517552/68‑1 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:316995/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:2667661/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:2888762/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:2904535/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:167261/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:995869/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:965367/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:972273/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:110313/1‑69 (MQ=255)
               ggTAAAAGAAGTTTTACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGaa                                                 >  1:972245/1‑69 (MQ=255)
                gTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGaa                                                 >  1:743372/1‑68 (MQ=255)
                gTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGaa                                                 >  1:3091337/1‑68 (MQ=255)
                  aaaaGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAAc                                              >  1:2129283/1‑69 (MQ=255)
                  aaaaGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAAc                                              >  1:2516597/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCagaaga                                                       >  1:2743158/1‑49 (MQ=37)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTc                                          >  1:804692/1‑62 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGtt                                    >  1:2721141/1‑68 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:518199/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:970886/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:2894640/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:2456862/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:2308667/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:2595479/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:336540/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:1614599/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:1784144/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:2064558/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:1839028/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:1979559/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:1114151/1‑69 (MQ=255)
                             tACGGCACCGTAATTTCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTc                                   >  1:1301206/1‑69 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCg                                      >  1:1464361/1‑62 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCggg                               >  1:789636/1‑69 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCggg                               >  1:959951/1‑69 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCggg                               >  1:2782898/1‑69 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCggg                               >  1:1751195/1‑69 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCggg                               >  1:1685413/1‑69 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCgg                                <  1:1430088/68‑1 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCgg                                <  1:3138613/68‑1 (MQ=255)
                                 tCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTATCCGAAGAGCGGAAAACAGTCTTCGTTCCgg                                <  1:2270851/68‑1 (MQ=255)
                                      gTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTg                           >  1:1758898/1‑68 (MQ=255)
                                      gTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTg                           >  1:163836/1‑68 (MQ=255)
                                           ttCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:1417990/69‑1 (MQ=255)
                                           ttCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:2161042/69‑1 (MQ=255)
                                           ttCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:3004661/69‑1 (MQ=255)
                                           ttCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:292017/69‑1 (MQ=255)
                                           ttCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:2711731/69‑1 (MQ=255)
                                           ttCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:2607751/69‑1 (MQ=255)
                                           ttCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:1089269/69‑1 (MQ=255)
                                            tCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGGCTTCGTTCCGGGACTGGCGAttt                    <  1:651723/69‑1 (MQ=255)
                                            tCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:3116060/68‑1 (MQ=255)
                                            tCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:291221/68‑1 (MQ=255)
                                            tCGCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:1729542/68‑1 (MQ=255)
                                              gCATCGCTGAGTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:3315812/66‑1 (MQ=255)
                                               cATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTa                  <  1:7151/68‑1 (MQ=255)
                                               cATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTa                  <  1:2252318/68‑1 (MQ=255)
                                               cATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTa                  <  1:1492221/68‑1 (MQ=255)
                                               cATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTa                  <  1:3344420/68‑1 (MQ=255)
                                               cATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTa                  <  1:331004/68‑1 (MQ=255)
                                               cATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGGGCCGGGACTGGCGATTTTa                  <  1:144369/68‑1 (MQ=255)
                                                  cGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGAttt                    <  1:1613907/63‑1 (MQ=255)
                                                    cTGAGTTTTCCAGGTCTTTCCGAAGAGCGGAATACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:1553490/60‑1 (MQ=255)
                                                        gTTTACCAGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCTGGACTGGCGAtt                     <  1:1082849/56‑1 (MQ=255)
                                                               gggTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATg  <  1:692240/68‑1 (MQ=255)
                                                               gggTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATg  <  1:1780966/68‑1 (MQ=255)
                                                               gggTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATg  <  1:2609918/68‑1 (MQ=255)
                                                               gggTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATg  <  1:116920/68‑1 (MQ=255)
                                                               gggTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATg  <  1:1917947/68‑1 (MQ=255)
                                                               gggTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATg  <  1:1987412/68‑1 (MQ=255)
                                                               |                                                                   
ACGTCTGGAAAAACTGGTAAAAGAAGTTTTACGTCACCGTAATTTCGCATCGCTGAGTTTACCGGGTCTTTCCGAAGAGCGGAAAACAGTCTTCGTTCCGGGACTGGCGATTTTATGCGGTGTGTTTGATG  >  minE/1658520‑1658650

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