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 1,284,104 C→T 42.2% V1961V (GTC→GTT)  yeeJ → adhesin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,284,1040CT42.2% 56.2 / 105.6 142V1961V (GTC→GTT) yeeJadhesin
Reads supporting (aligned to +/- strand):  ref base C (52/30);  new base T (14/46);  total (66/76)
Fisher's exact test for biased strand distribution p-value = 3.13e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.29e-01

Only 100 of 151 total aligned reads displayed.

GGTACATATACGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGC  >  minE/1284036‑1284163
                                                                    |                                                           
ggTACATATACGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTc                                                             <  1:1645082/69‑1 (MQ=255)
ggTACATATACGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTc                                                             <  1:2153290/69‑1 (MQ=255)
ggTACATATACGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTc                                                             <  1:737677/69‑1 (MQ=255)
ggTACATATACGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTCAAAGTc                                                             <  1:435699/69‑1 (MQ=255)
      tataCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGc                                                       >  1:2612205/1‑69 (MQ=255)
      tataCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGc                                                       >  1:1810959/1‑69 (MQ=255)
      tataCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGc                                                       >  1:2712082/1‑69 (MQ=255)
       ataCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCa                                                      <  1:3237250/69‑1 (MQ=255)
        taCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCaa                                                     >  1:2251937/1‑69 (MQ=255)
        taCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCaa                                                     >  1:2678014/1‑69 (MQ=255)
        taCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCaa                                                     >  1:853672/1‑69 (MQ=255)
        taCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCaa                                                     >  1:687200/1‑69 (MQ=255)
        taCGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCa                                                      <  1:743578/68‑1 (MQ=255)
            gTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCa                                                 <  1:1168627/69‑1 (MQ=255)
            gTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCa                                                 <  1:1571072/69‑1 (MQ=255)
                       tttCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                      >  1:1241583/1‑69 (MQ=255)
                           cATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                      <  1:3397578/65‑1 (MQ=255)
                           cATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                      <  1:2792111/65‑1 (MQ=255)
                           cATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                      <  1:2397105/65‑1 (MQ=255)
                               aCGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCt                               >  1:1815947/1‑68 (MQ=255)
                               aCGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTa                              >  1:1706493/1‑69 (MQ=255)
                                 ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                            >  1:1889943/1‑69 (MQ=255)
                                 ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                            >  1:281650/1‑69 (MQ=255)
                                 ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                            >  1:1705178/1‑69 (MQ=255)
                                 ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                            >  1:1090379/1‑69 (MQ=255)
                                 ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                            >  1:841766/1‑69 (MQ=255)
                                 ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                            >  1:426715/1‑69 (MQ=255)
                                 ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                            <  1:1263562/69‑1 (MQ=255)
                                    gtcaCAATACAGACACAGATAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:2204535/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:2788779/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:848103/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:2903242/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:601545/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:3004057/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:1690874/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:3157958/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:3195167/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:523499/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:3271160/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:1193529/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:1867221/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:1834730/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:244441/66‑1 (MQ=255)
                                    gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                         <  1:1615067/66‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:95081/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:3066497/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:81608/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:522026/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:45563/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:3308477/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:980217/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:2587025/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1515444/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1575628/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1652571/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1942884/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1983894/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1993847/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1291701/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:2451561/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:2261118/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                      <  1:1196447/69‑1 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATc                      >  1:771484/1‑69 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATc                      >  1:786642/1‑69 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATc                      >  1:1924680/1‑69 (MQ=255)
                                       aCAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATc                      >  1:2296253/1‑69 (MQ=255)
                                            acagacacagacAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGa                 >  1:5151/1‑69 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGc                                         >  1:1444211/1‑44 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                         <  1:3099334/60‑1 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                         <  1:3383530/60‑1 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                         <  1:380671/60‑1 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                  >  1:3119245/1‑67 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                  >  1:2410764/1‑67 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                  >  1:82770/1‑67 (MQ=255)
                                             cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                  >  1:502280/1‑67 (MQ=255)
                                               gacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATcc              <  1:797289/69‑1 (MQ=255)
                                                   cagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                         <  1:2203479/54‑1 (MQ=255)
                                                     gacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGAc        >  1:1734703/1‑69 (MQ=255)
                                                     gacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGAc        >  1:2070052/1‑69 (MQ=255)
                                                     gacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGAc        >  1:1432185/1‑69 (MQ=255)
                                                       caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa      >  1:2238324/1‑69 (MQ=255)
                                                       caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa      >  1:1398825/1‑69 (MQ=255)
                                                       caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa      >  1:2735281/1‑69 (MQ=255)
                                                       caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa      >  1:317396/1‑69 (MQ=255)
                                                         aCCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATc    <  1:1026425/69‑1 (MQ=255)
                                                         aCCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATc    <  1:2695576/69‑1 (MQ=255)
                                                         aCCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATc    <  1:2485235/69‑1 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:1447427/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:1595098/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:1386683/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:3096995/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:790081/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:3088546/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:1326864/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:201990/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:1301504/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:3004898/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc              >  1:1171693/1‑58 (MQ=255)
                                                          ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATc               >  1:3370054/1‑57 (MQ=255)
                                                           cGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATcgc  >  1:1545416/1‑69 (MQ=255)
                                                                    |                                                           
GGTACATATACGGTGACTGCATCTTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGC  >  minE/1284036‑1284163

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