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 F28 I1 R1 58 121.6 3649812 78.1% 2850503 56.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 1,468,989 C→G W911C (TGG→TGC)  yfaL ← adhesin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,468,9890CG99.6% 946.6 / NA 243W911C (TGG→TGC) yfaLadhesin
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base G (118/124);  total (119/124)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 243 total aligned reads displayed.

GGGAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATACCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATATT  >  minE/1468932‑1469036
                                                         |                                               
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAg                                              >  1:1575174/1‑61 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAg                                              >  1:21329/1‑61 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAg                                              >  1:2266978/1‑61 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGt                                             >  1:2448502/1‑62 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGt                                             >  1:2025074/1‑62 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGt                                             >  1:1305447/1‑62 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGt                                             >  1:2173785/1‑62 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTAATTCTTGCGATCGCAGATAGCAGt                                             >  1:1416206/1‑62 (MQ=255)
gggAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTA‑TTCTTGCGATCGCAGATAGCAGTc                                            >  1:1929419/1‑62 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:1822000/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:1006710/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:3024140/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2932012/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2276626/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2786877/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2754744/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2428997/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2519223/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2678303/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:2622252/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:3620188/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:855320/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:1388382/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:1213992/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:35371/61‑1 (MQ=255)
  gAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:487161/61‑1 (MQ=255)
  gAGTCGGGGCTGGATCAGGGGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:3633471/61‑1 (MQ=255)
   aGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTc                                            <  1:1252300/60‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATGGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2841137/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCTTTGTTATCTTCCACCAGc                         <  1:312672/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:980123/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2746946/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:370827/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:606055/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2814499/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:934075/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3366892/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2865010/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3552004/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2980807/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3502403/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3422299/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:308000/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3398303/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:316385/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3168623/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3250093/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:3267061/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:1936946/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:1631300/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:1603840/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:154045/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:150084/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:1178774/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:1940890/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2013634/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2123471/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2218578/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:2303476/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:1152340/62‑1 (MQ=255)
                    gTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:1057893/62‑1 (MQ=255)
                     tGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGc                         <  1:76789/61‑1 (MQ=255)
                                    tACTTCTTGCGATCGCAGATAGCAGTCGTTGTTAt                                    >  1:456329/1‑35 (MQ=255)
                                    tACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCt          >  1:1021919/1‑61 (MQ=255)
                                    tACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCt          >  1:548129/1‑61 (MQ=255)
                                    tACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCt          >  1:1450253/1‑61 (MQ=255)
                                    tACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCt          >  1:3482870/1‑61 (MQ=255)
                                    tACTTCTTGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCt          >  1:1781956/1‑61 (MQ=255)
                                      cttcttGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTcc        >  1:2539455/1‑61 (MQ=255)
                                      cttcttGCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTcc        >  1:2375925/1‑61 (MQ=255)
                                            gtgATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:3193105/3‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCatat   >  1:1496202/1‑60 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:2425205/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:91910/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:963482/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:83229/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:802794/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1288310/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:790268/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:2087605/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:736287/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:693873/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:649934/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1863987/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:585322/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:3120415/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:536373/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:3309014/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1854034/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1344615/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1817960/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1454125/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:3584603/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:3522983/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1754167/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:34717/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:3452204/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:156082/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:1684804/1‑61 (MQ=255)
                                            gCGATCGCAGATAGCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATAtt  >  1:3300780/1‑61 (MQ=255)
                                                         |                                               
GGGAGTCGGGTCTGGATCAGGTGGCGATGGCGGCGTTACTTCTTGCGATCGCAGATACCAGTCGTTGTTATCTTCCACCAGCGTGTAGTCATACGCTCCCATATT  >  minE/1468932‑1469036

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