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 2,251,037 T→A 51.8% L173L (CTT→CTA)  thiH → thiamin biosynthesis ThiGH complex subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,251,0370TA51.8% 6.6 / 139.0 114L173L (CTT→CTA) thiHthiamin biosynthesis ThiGH complex subunit
Reads supporting (aligned to +/- strand):  ref base T (14/41);  new base A (54/5);  total (68/46)
Fisher's exact test for biased strand distribution p-value = 1.36e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

Only 100 of 114 total aligned reads displayed.

TCTCTTCACTACAGATGGAAGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACTTATGCCCGCC  >  minE/2250973‑2251095
                                                                |                                                          
tctcTTCACTACAGATGGAAGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTc                                                        >  1:1030489/1‑69 (MQ=255)
      cACTACAGATGGAAGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATg                                                  >  1:1140820/1‑69 (MQ=255)
      cACTACAGATGGAAGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATg                                                  >  1:241661/1‑69 (MQ=255)
      cACTACAGATGGAAGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATg                                                  >  1:3112248/1‑69 (MQ=255)
                   aGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGttt                                      >  1:2711151/1‑68 (MQ=255)
                   aGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGttt                                      >  1:164356/1‑68 (MQ=255)
                   aGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGttt                                      >  1:1495427/1‑68 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATc                                   >  1:2866419/1‑67 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATc                                   >  1:2151478/1‑67 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATc                                   >  1:1362540/1‑67 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATc                                   <  1:1901006/67‑1 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATc                                   <  1:3429530/67‑1 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATc                                   <  1:443998/67‑1 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATc                                   <  1:1123393/67‑1 (MQ=255)
                       cAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATc                                   <  1:742598/67‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:2600950/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:3140529/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:2273343/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:1202534/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:2478656/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:3090842/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:210043/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:367527/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:2738640/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:372879/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:820901/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:51257/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:1057415/69‑1 (MQ=255)
                           cGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGgaga                             <  1:1416267/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:2899815/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:180665/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:1711817/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:2651343/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:45597/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:3311270/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:2268931/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:2311831/69‑1 (MQ=255)
                              tGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:919348/69‑1 (MQ=255)
                               ggCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:357679/68‑1 (MQ=255)
                               ggCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:918374/68‑1 (MQ=255)
                               ggCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACat                          <  1:1914470/68‑1 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCACCTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:3362588/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:2687371/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:727829/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:3164850/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:901205/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:2689701/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:52144/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:527641/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:2143123/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:1640974/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:2350928/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:1626731/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:1270174/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:2296121/1‑68 (MQ=255)
                                  ggAGACGGAATACGCCGAGTTAAAGAAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATc                       >  1:1212011/1‑68 (MQ=255)
                                        ggAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATgg                                         <  1:704109/44‑1 (MQ=255)
                                        ggAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATgg                                         <  1:2637695/44‑1 (MQ=255)
                                        ggAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATgg                                         <  1:449162/44‑1 (MQ=255)
                                            tACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACt            <  1:92088/69‑1 (MQ=255)
                                            tACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACt            <  1:2891762/69‑1 (MQ=255)
                                            tACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACt            <  1:3056579/69‑1 (MQ=255)
                                            tACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGACGGTTTATCAGGAGACATATCACGAGGCGACt            <  1:412738/69‑1 (MQ=255)
                                             aCGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACt            <  1:2654145/68‑1 (MQ=255)
                                             aCGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACt            <  1:214375/68‑1 (MQ=255)
                                                  gAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACTTAt         <  1:1873096/66‑1 (MQ=255)
                                                      tAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACTTATGCCGGcc  <  1:2076189/69‑1 (MQ=255)
                                                      tAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACTTATGCCCGcc  <  1:480671/69‑1 (MQ=255)
                                                      tAAAGCAACTAGGTCTGTATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACtt           >  1:3401432/1‑60 (MQ=255)
                                                      tAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACtt           >  1:3432822/1‑60 (MQ=255)
                                                      tAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACtt           >  1:175704/1‑60 (MQ=255)
                                                      tAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACtt           >  1:478669/1‑60 (MQ=255)
                                                      tAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACtt           >  1:899120/1‑60 (MQ=255)
                                                      tAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACtt           >  1:928183/1‑60 (MQ=255)
                                                      tAAAGCAACTAGGTCTGGATGGCGTGATGGTTTATAAGGAGACATATCACGAGGCGACtt           >  1:1023044/1‑60 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGGGACATATCACGAGGCGAc             >  1:2829095/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:1441233/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:985736/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2665798/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2661699/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:1229040/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:1259503/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2788227/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:751337/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:1435337/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2126027/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:1621257/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2831993/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2870720/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2877407/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2513469/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2935064/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2498581/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2400375/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:380713/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2215432/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:3348051/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCTGGATGGCGTGATCGTTTATCAg                                 >  1:276693/1‑37 (MQ=37)
                                                       aaaGCAACTAGGTCTGCATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGAc             >  1:2767072/1‑57 (MQ=255)
                                                       aaaGCAACTAGGTCAGGATGGCGTGATGGTTTATCAGGAGACATATCa                      >  1:1363314/1‑48 (MQ=39)
                                                                |                                                          
TCTCTTCACTACAGATGGAAGTGCAACCGCTGGCGGAGACGGAATACGCCGAGTTAAAGCAACTTGGTCTGGATGGCGTGATGGTTTATCAGGAGACATATCACGAGGCGACTTATGCCCGCC  >  minE/2250973‑2251095

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