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 2,720,417 C→A 61.5% L388L (CTG→CTT)  yhfK ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,720,4170CA61.5% 31.6 / 57.4 65L388L (CTG→CTT) yhfKconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (22/3);  new base A (15/25);  total (37/28)
Fisher's exact test for biased strand distribution p-value = 7.76e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

ATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAACATCA  >  minE/2720363‑2720454
                                                      |                                     
aTTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGcac                           <  1:2961557/67‑3 (MQ=255)
aTTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCAt                         <  1:2537246/69‑1 (MQ=255)
   ttGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAg                      >  1:2666117/1‑69 (MQ=255)
   ttGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAg                      >  1:163139/1‑69 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:1861462/1‑68 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:2999726/1‑68 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:34572/1‑68 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:165541/1‑68 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:101813/1‑68 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:2362532/1‑68 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:1300432/1‑68 (MQ=255)
        tCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTg                  >  1:1266342/1‑68 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAgc                                    >  1:1083234/1‑48 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGc                >  1:2072536/1‑68 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa               >  1:2415206/1‑69 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa               >  1:2305690/1‑69 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa               >  1:1225798/1‑69 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa               >  1:2629825/1‑69 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa               >  1:205312/1‑69 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCa               >  1:2038795/1‑69 (MQ=255)
          aCCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCAACAGGCTGGCa               >  1:2664843/1‑69 (MQ=255)
             aGCAATTCTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:439285/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGTCAACg            >  1:2818111/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAAc             >  1:2074186/1‑68 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:3040342/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:1841180/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:1560639/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:2082796/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:976443/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:1700233/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:1580990/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:2129973/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:91146/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:2260946/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATCCAGTAAGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:791387/1‑69 (MQ=255)
             aGCAATACTGTCATCAGGATACAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACg            >  1:1920057/1‑69 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:3025712/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:811347/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:2128356/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:810226/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:2853626/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:510614/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:285506/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:3237501/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:3180789/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:2481854/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1058988/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:109856/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1216817/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1415707/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1425729/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1786750/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1800525/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1846014/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1894956/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:2092407/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:2097184/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:2171239/69‑1 (MQ=255)
                aaTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCACATCAGGCTGGCAACGCtt         <  1:3297503/69‑1 (MQ=255)
                 aTACTGTCATCAGGATCCAGTACGACTTCGGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:1698358/68‑1 (MQ=255)
                 aTACTGTCATCAGGATCCAGTACGACTTCAGCAGATGAAGCGCGGTGCCCATCAGGCTGGCAACGCtt         <  1:411023/68‑1 (MQ=255)
                   aCCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAc      >  1:1528162/1‑69 (MQ=255)
                   aCCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAc      >  1:27504/1‑69 (MQ=255)
                    ccGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAAc      >  1:914115/1‑68 (MQ=255)
                       tcatcaGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAACATca  <  1:1406073/69‑1 (MQ=255)
                                                      |                                     
ATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGTACGACTTCGGCAGATGCAGCGCGGTGCCCATCAGGCTGGCAACGCTTAACATCA  >  minE/2720363‑2720454

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