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 375,669 G→A 56.4% R139R (CGC→CGT)  fepG ← iron‑enterobactin transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE375,6690GA56.4% 14.7 / 54.7 71R139R (CGC→CGT) fepGiron‑enterobactin transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (6/25);  new base A (20/20);  total (26/45)
Fisher's exact test for biased strand distribution p-value = 1.24e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGACAATGCCGCCCACCATTGCTGACAGCGC  >  minE/375603‑375731
                                                                  |                                                              
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:2406200/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:32287/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:3158485/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:3399880/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:1589432/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:620151/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:2277591/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:1081997/1‑68 (MQ=255)
aaaGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTgc                                                               >  1:935784/1‑68 (MQ=255)
          agtaTGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCg                                                       >  1:405857/4‑66 (MQ=255)
          agtaTGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGagc                                                    >  1:312338/4‑69 (MQ=255)
          agtaTGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGagc                                                    >  1:3264694/4‑69 (MQ=255)
                              accgataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGt                                >  1:690673/1‑69 (MQ=255)
                              accgataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGt                                >  1:3363291/1‑69 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:2673838/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:2817862/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:3103346/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:2593916/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:3215709/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:3265346/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:3237681/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:3256599/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:3261527/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:104282/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:438382/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:587663/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:592019/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:658801/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:858278/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:972746/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:23670/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:135071/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:1374764/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:2397195/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:1660678/69‑1 (MQ=255)
                                 gataATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:2137833/69‑1 (MQ=255)
                                 cataataATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:889757/68‑1 (MQ=255)
                                          cAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGAc                             <  1:176469/60‑1 (MQ=255)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCa                                               >  1:2833354/1‑39 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:227568/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:507496/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:466582/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:425016/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:415283/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:412397/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:617058/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:2481296/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:34972/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:1061607/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:2327920/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:3284372/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:1237434/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:1702607/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:120621/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:1921245/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:206192/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:2625750/1‑41 (MQ=37)
                                             ccGAAAGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGa                                             >  1:937244/1‑41 (MQ=37)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:678974/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:114378/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:930972/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:782365/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:1100203/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:588767/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:1329392/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:515284/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:2419992/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:1690977/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:1715431/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:2075071/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:2207793/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:2901859/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:2856077/69‑1 (MQ=255)
                                                 aaGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:2243658/69‑1 (MQ=255)
                                                 aaGGTGTCGATACAGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:390539/69‑1 (MQ=255)
                                                  aGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:827495/68‑1 (MQ=255)
                                                  aGGTGTCGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:1628249/68‑1 (MQ=255)
                                                      gtCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGACAATGCCGCCCACCATTGCt          >  1:1007972/1‑67 (MQ=255)
                                                        cGATACCGTTACGCCAGGCGAGCAGCCAGACCAACAGCGAAGTGACAATGCCGCCCACCAtt             <  1:216279/62‑1 (MQ=255)
                                                            gCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGACAATGCCGCCCACCATTGCTGACAgcgc  <  1:1286300/69‑1 (MQ=255)
                                                                  |                                                              
AAAGGCCACCAGCATGGCGCGAACGCCGATACCGATAATAATCAACCGAAAGGTGTCGATGCCGTTGCGCCAGGCGAGCAGCCAGACCAGCAGCGAAGTGACAATGCCGCCCACCATTGCTGACAGCGC  >  minE/375603‑375731

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