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 2,200,413 C→G 30.0% D143E (GAC→GAG)  argR → DNA‑binding transcriptional dual regulator, L‑arginine‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,200,4130CG30.0% 126.9 / 65.5 100D143E (GAC→GAG) argRDNA‑binding transcriptional dual regulator, L‑arginine‑binding
Reads supporting (aligned to +/- strand):  ref base C (47/23);  new base G (24/6);  total (71/29)
Fisher's exact test for biased strand distribution p-value = 2.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

Only 100 of 108 total aligned reads displayed.

ATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCCGTCGTTTCTG  >  minE/2200345‑2200475
                                                                    |                                                              
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:1739609/69‑1 (MQ=255)
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:2618271/69‑1 (MQ=255)
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:1858191/69‑1 (MQ=255)
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:2192949/69‑1 (MQ=255)
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:1881975/69‑1 (MQ=255)
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:1966639/69‑1 (MQ=255)
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:2142825/69‑1 (MQ=255)
aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                                                <  1:745309/69‑1 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:1450439/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:422892/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:3281508/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:3245695/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:3063008/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:3017182/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:2173666/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:835810/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:1092159/1‑69 (MQ=255)
            aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                                                    >  1:977436/1‑69 (MQ=255)
                 tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                                                <  1:2349836/68‑1 (MQ=255)
                 tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                                                <  1:2644965/68‑1 (MQ=255)
                 tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                                                <  1:1354021/68‑1 (MQ=255)
                 tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                                                <  1:833367/68‑1 (MQ=255)
                 tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                                                <  1:816822/68‑1 (MQ=255)
                 tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                                                <  1:976177/68‑1 (MQ=255)
                  ggCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                                              <  1:463315/69‑1 (MQ=255)
                  ggCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                                              <  1:543207/69‑1 (MQ=255)
                  ggCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                                              <  1:2060123/69‑1 (MQ=255)
                   gCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                                              <  1:1775896/68‑1 (MQ=255)
                   gCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                                              <  1:3347565/68‑1 (MQ=255)
                     gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                                           >  1:540286/1‑69 (MQ=255)
                     gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                                           >  1:141223/1‑69 (MQ=255)
                     gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                                           >  1:2622914/1‑69 (MQ=255)
                     gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                                           >  1:167177/1‑69 (MQ=255)
                     gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                                           >  1:58832/1‑69 (MQ=255)
                     gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                                           >  1:3416323/1‑69 (MQ=255)
                       tGACACCATCTTTACTACCCCTGCTAACTGTTTCACCGTCAAAGAGCTg                                                             >  1:195965/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCt                                                              >  1:3063877/1‑48 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:962104/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:2722062/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:541548/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:1054745/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:2897518/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:2978166/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:870366/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:3007790/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:741932/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:683295/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:3342834/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:664050/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:3411267/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:1682244/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:2107426/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:2056329/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:216567/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:1751675/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:1642961/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:1159966/1‑49 (MQ=37)
                       tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                                             >  1:1026490/1‑49 (MQ=37)
                        gACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg                                        <  1:9243/69‑1 (MQ=255)
                        gACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg                                        <  1:1753466/69‑1 (MQ=255)
                        gACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg                                        <  1:1105570/69‑1 (MQ=255)
                         acacCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg                                        <  1:217935/68‑1 (MQ=255)
                           acCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTc                                     <  1:178404/69‑1 (MQ=255)
                                 tttACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg                                        >  1:2633055/1‑60 (MQ=255)
                                 tttACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGAcc                                 >  1:1578213/1‑67 (MQ=255)
                                 tttACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGAcc                                 >  1:770009/1‑67 (MQ=255)
                                     ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGAGCAGGAg                            <  1:435904/68‑1 (MQ=255)
                                     ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:38618/68‑1 (MQ=255)
                                     ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:2443505/68‑1 (MQ=255)
                                     ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:3197044/68‑1 (MQ=255)
                                     ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:3132679/68‑1 (MQ=255)
                                     ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:2132053/68‑1 (MQ=255)
                                     ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:227021/68‑1 (MQ=255)
                                      caccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:670487/67‑1 (MQ=255)
                                        ccccTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCttt                        >  1:1768535/1‑69 (MQ=255)
                                        ccccTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCttt                        >  1:2307245/1‑69 (MQ=255)
                                            tGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtc                    >  1:343763/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:2308843/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:1541338/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:951101/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:2325777/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:2507468/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:1199654/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:4454/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:2128836/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:3415185/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:1823929/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:2118948/1‑69 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtct                   >  1:1225874/1‑68 (MQ=255)
                                              cTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTACAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:1579324/1‑69 (MQ=255)
                                              cTAACGGTTTCAAAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAAtctc                  >  1:1744487/1‑69 (MQ=255)
                                                   ggTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:2332287/54‑1 (MQ=255)
                                                       tCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg                            <  1:2280479/50‑1 (MQ=255)
                                                       tCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCcgtc         >  1:2457111/1‑69 (MQ=255)
                                                       tCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCcgtc         >  1:1376246/1‑69 (MQ=255)
                                                       tCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCcgtc         >  1:673270/1‑69 (MQ=255)
                                                       tCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCcgtc         >  1:1949435/1‑69 (MQ=255)
                                                              cAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCCGTCGTTTCt   >  1:1519853/1‑68 (MQ=255)
                                                              cAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCCGTCGTTTCTg  >  1:2530843/1‑69 (MQ=255)
                                                              cAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCCGTCGTTTCTg  >  1:1710579/1‑69 (MQ=255)
                                                                    |                                                              
ATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAGCTTTAATCTCTGCCCCGTCGTTTCTG  >  minE/2200345‑2200475

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