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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 385,153 C→G 31.6% L121L (CTC→CTG)  cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE385,1530CG31.6% 72.0 / 47.8 61L121L (CTC→CTG) cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base C (14/27);  new base G (7/12);  total (21/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.83e-01

CAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTC  >  minE/385086‑385223
                                                                   |                                                                      
cAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCt                                                                     <  1:1548247/71‑1 (MQ=255)
    tCCGCTGGTGGGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGcg                                                                     >  1:4242236/1‑66 (MQ=255)
      cGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTAGCTGGggt                                                                <  1:4945212/70‑1 (MQ=255)
       gCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGggtgg                                                              <  1:2738382/71‑1 (MQ=255)
        cTGGTGGGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGggtcgt                                                             <  1:3437747/71‑1 (MQ=255)
           gtggGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTgct                                                          >  1:3439234/1‑71 (MQ=255)
           gtggGTCCGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTgct                                                          >  1:449019/1‑71 (MQ=255)
              ggtccGGTTCTCGCCGCGCAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGc                                                       >  1:3274463/4‑71 (MQ=255)
               ggCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGcc                                                      <  1:5507184/71‑1 (MQ=255)
                    gTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCg                                                                       <  1:1648172/49‑1 (MQ=255)
                     tACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGggtgg                                                              <  1:5656408/57‑1 (MQ=255)
                     tACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGCCTGCTCGCTGGggtgg                                                              <  1:3690331/57‑1 (MQ=255)
                      aCTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTgg                                                                   >  1:4122070/1‑51 (MQ=255)
                      aCTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtgcg                                                >  1:4901219/1‑70 (MQ=255)
                       cTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTtctc                                                         >  1:2271265/1‑60 (MQ=255)
                         ggcggcGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTtctc                                                         >  1:3012489/1‑58 (MQ=255)
                          gcggcgCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtgcggtg                                             >  1:1625793/1‑69 (MQ=255)
                          gccgcgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCcggtgcggt                                              <  1:1569900/65‑1 (MQ=255)
                          gccgcgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCcggtgcggt                                              <  1:12417/65‑1 (MQ=255)
                             gcgcAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAg                                          <  1:2642605/69‑1 (MQ=255)
                              cgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGac                                       <  1:3892571/71‑2 (MQ=255)
                              cgcAGATGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGac                                       <  1:4336456/71‑2 (MQ=255)
                               gcAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAtt                                      >  1:5187398/1‑71 (MQ=255)
                                cagaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActt                                     <  1:4055455/68‑1 (MQ=255)
                                cAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTggg                                                                  <  1:1156919/42‑1 (MQ=255)
                                cAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTggg                                                                  <  1:4314084/42‑1 (MQ=255)
                                cAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                                     <  1:1112480/71‑1 (MQ=255)
                                  gaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActtta                                   >  1:3683789/2‑69 (MQ=255)
                                  gaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActtta                                   <  1:1917284/70‑3 (MQ=255)
                                  gaTGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGActtta                                   <  1:5612495/70‑3 (MQ=255)
                                  aaTGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGtggtgg                                                              <  1:4952236/44‑1 (MQ=255)
                                  aaTGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGggtgg                                                              <  1:890215/44‑1 (MQ=255)
                                    tGGGCTACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATg                                 <  1:4973445/71‑1 (MQ=255)
                                    tGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTAGCCGGTGCGGTGCAGGATTTCATg                                 >  1:5038970/1‑71 (MQ=255)
                                         tACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCt                            >  1:268300/1‑71 (MQ=255)
                                         tACCTGCCTGGCACGCTGTGGCTGCTGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCt                            >  1:2429487/1‑71 (MQ=255)
                                           ccTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCtgt                          <  1:3102020/71‑1 (MQ=255)
                                            cTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCtgtt                         >  1:4242997/1‑71 (MQ=255)
                                             tGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcg                                                     >  1:5497278/1‑42 (MQ=255)
                                             tGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcg                                                     >  1:3477614/1‑42 (MQ=255)
                                               ccGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                                     <  1:808785/56‑1 (MQ=255)
                                               ccGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCtgtttgt                      >  1:4970713/1‑71 (MQ=255)
                                                 ggggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCa                                   >  1:890358/1‑56 (MQ=255)
                                                 ggggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCa                                   >  1:3114377/1‑56 (MQ=255)
                                                  gggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtg                                                  <  1:247791/40‑1 (MQ=255)
                                                  gggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtg                                                  <  1:4303072/40‑1 (MQ=255)
                                                  gggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCcggtg                                                  <  1:4647609/40‑1 (MQ=255)
                                                   ggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCt                  <  1:416204/71‑1 (MQ=255)
                                                   ggATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCt                  <  1:3221073/71‑1 (MQ=255)
                                                    gatgatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCt                  <  1:356398/70‑1 (MQ=255)
                                                       gatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTAcgc              >  1:4146158/1‑71 (MQ=255)
                                                        atCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                                     <  1:3860205/47‑1 (MQ=255)
                                                        atCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGAttt                                     <  1:3721332/47‑1 (MQ=255)
                                                           tGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGTTGCAGGAtt                                      <  1:3479728/43‑1 (MQ=255)
                                                             gctgctGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCTGTTTATCTCCTCTCGCCGt         <  1:1542498/70‑1 (MQ=255)
                                                             gctgctGGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCTGTTTATCTCCTCTCGCCGt         <  1:3090677/70‑1 (MQ=255)
                                                             gctgctGGCGGGGGGCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCTGTTTATCTCCTCTCGCCGt         <  1:500199/70‑1 (MQ=255)
                                                             gctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGcc           <  1:4305117/68‑1 (MQ=255)
                                                             gctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGt         <  1:3200192/70‑1 (MQ=255)
                                                             gctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGt         <  1:4418362/70‑1 (MQ=255)
                                                             gctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGt         <  1:2458152/70‑1 (MQ=255)
                                                              ctgctgGCGGGGGTCGTGCTGGCCGGTGCGGTTCAGGACTTTATGGTGCtgttt                        <  1:1922410/54‑1 (MQ=255)
                                                                   cGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGtc  >  1:5490728/1‑71 (MQ=255)
                                                                   |                                                                      
CAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTC  >  minE/385086‑385223

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