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 1,672,344 A→C 49.6% A306A (GCT→GCG)  hisS ← histidyl tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,672,3440AC49.6% 9.2 / 134.2 103A306A (GCT→GCG) hisShistidyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base A (28/24);  new base C (42/9);  total (70/33)
Fisher's exact test for biased strand distribution p-value = 2.88e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

Only 100 of 103 total aligned reads displayed.

CGGCTTTAAATTCCGGATTAACGGCCTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAACGACCG  >  minE/1672286‑1672407
                                                          |                                                               
cGGCTTTAAATTCCGGATTAACGGCCTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAAcc                                                         >  1:1954412/1‑67 (MQ=255)
cGGCTTTAAATTCCGGATTAACGGCCTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAAcc                                                         >  1:2851349/1‑67 (MQ=255)
cGGCTTTAAATTCCGGATTAACGGCCTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAAcc                                                         >  1:3125361/1‑67 (MQ=255)
cGGCTTTAAATTCCGGATTAACGGCCTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAAcc                                                         >  1:418616/1‑67 (MQ=255)
                aTTAACGGCCTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACg                                       <  1:192093/69‑1 (MQ=255)
                         cTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAACCCGACAGCCGGTGTTGCACGACCGCCCAg                              <  1:2281832/69‑1 (MQ=255)
                         cTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAg                              <  1:460308/69‑1 (MQ=255)
                         cTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAg                              <  1:667023/69‑1 (MQ=255)
                         cTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAg                              <  1:2139023/69‑1 (MQ=255)
                         cTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAg                              <  1:2255711/69‑1 (MQ=255)
                         cTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAg                              <  1:1404452/69‑1 (MQ=255)
                              cTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGCCCGCCCAg                              >  1:684259/1‑64 (MQ=255)
                              cTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAgttgt                          >  1:3355469/1‑68 (MQ=255)
                              cTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAgttgt                          >  1:1838497/1‑68 (MQ=255)
                              cTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAgttgt                          >  1:2275247/1‑68 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:2935790/69‑1 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:2707096/69‑1 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:20512/69‑1 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:2311112/69‑1 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:1251622/69‑1 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:1829941/69‑1 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:817941/69‑1 (MQ=255)
                               tAACAATACAAGACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:864342/69‑1 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        <  1:389621/68‑1 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        <  1:2106995/68‑1 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        <  1:1612090/68‑1 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        >  1:226158/1‑68 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        <  1:1395720/68‑1 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        <  1:1899059/68‑1 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        >  1:314957/1‑68 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        >  1:2728569/1‑68 (MQ=255)
                                aaCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        <  1:1421096/68‑1 (MQ=255)
                                 aCAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTc                        <  1:448684/67‑1 (MQ=255)
                                    aTACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTT‑CACGACCGCCCAGTTGTTCCACAAg                  <  1:891683/69‑1 (MQ=255)
                                     tACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAg                  <  1:834426/69‑1 (MQ=255)
                                      aCAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAg                  <  1:2480970/68‑1 (MQ=255)
                                      aCAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAg                  <  1:2220260/68‑1 (MQ=255)
                                      aCAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGa                 >  1:3297168/1‑69 (MQ=255)
                                      aCAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGa                 >  1:3326147/1‑69 (MQ=255)
                                       cAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGAc                >  1:2949882/1‑69 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACg                                       >  1:1451887/1‑43 (MQ=38)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:1091622/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:899628/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:895755/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:310196/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:2695629/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:3151085/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:3062105/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:3210797/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:2516845/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:1090103/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:1040720/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:101093/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:1165109/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:1207152/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:1266857/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:2212807/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:858861/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:690950/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:192743/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:425949/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:2013116/1‑67 (MQ=255)
                                          gACGTTCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACCACCACCCAGTTGTTCCACCAGACCg              >  1:1719740/1‑68 (MQ=255)
                                          gACGTTCGAGACCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGAcc               >  1:1547930/1‑67 (MQ=255)
                                             gTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAg                              <  1:1139214/49‑1 (MQ=255)
                                               tggAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:2359302/3‑68 (MQ=255)
                                               tCGAGGTCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:439367/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCAt          >  1:125956/1‑67 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:2259009/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:1845543/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:1947515/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:2833430/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:2015803/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:1804805/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:1667968/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:1552378/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:2346383/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:1447172/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:2701098/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:2806885/1‑68 (MQ=255)
                                               tCGAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:942618/1‑68 (MQ=255)
                                               tCGAGGACCATAGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTCCACCAGACCGTCATa         >  1:437280/1‑68 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGa                                      >  1:1093853/1‑38 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACaa                   >  1:259884/1‑57 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCAt          >  1:2000975/1‑66 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCAt          >  1:1150667/1‑66 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCAt          >  1:609339/1‑66 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCAt          >  1:2056806/1‑66 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCAt          >  1:2786561/1‑66 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAAc       >  1:782818/1‑69 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAAc       >  1:2104048/1‑69 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAAc       >  1:3387797/1‑69 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAAc       >  1:311717/1‑69 (MQ=255)
                                                cGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAAc       >  1:281572/1‑69 (MQ=255)
                                                 gAGGCCCATCGCAAAACCGACTGCCGGTGTTGCACGACCACCCAGTTGTTc                        <  1:2411168/51‑1 (MQ=255)
                                                     cccATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAACGACCg  <  1:1936059/69‑1 (MQ=255)
                                                     cccATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAACGACCg  <  1:783147/69‑1 (MQ=255)
                                                     cccATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAACGACCg  <  1:174169/69‑1 (MQ=255)
                                                     cccATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAACGACCg  <  1:873051/69‑1 (MQ=255)
                                                     cccATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAACGACCg  <  1:2637901/69‑1 (MQ=255)
                                                          |                                                               
CGGCTTTAAATTCCGGATTAACGGCCTGTACTAACAATACAAGACGTTCGAGGCCCATAGCAAAACCGACAGCCGGTGTTGCACGACCGCCCAGTTGTTCCACAAGACCGTCATAACGACCG  >  minE/1672286‑1672407

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