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 2,200,383 C→T 36.5% T133T (ACC→ACT)  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
*minE2,200,3830CT36.5% 52.2 / 49.1 82T133T (ACC→ACT) argRDNA‑binding transcriptional dual regulator, L‑arginine‑binding
Reads supporting (aligned to +/- strand):  ref base C (33/19);  new base T (24/6);  total (57/25)
Fisher's exact test for biased strand distribution p-value = 1.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.02e-01

ACTGGGCAAAGCAGAAGGTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAG  >  minE/2200326‑2200449
                                                         |                                                                  
aCTGGGCAAAGCAGAAGGTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTaa                                                         >  1:1355708/1‑69 (MQ=255)
                ggTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCaaa                                         >  1:369296/1‑69 (MQ=255)
                ggTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCaaa                                         >  1:608338/1‑69 (MQ=255)
                ggTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCaaa                                         >  1:1342093/1‑69 (MQ=255)
                ggTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCaaa                                         >  1:3005433/1‑69 (MQ=255)
                ggTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCaaa                                         >  1:874862/1‑69 (MQ=255)
                  tATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGa                                       >  1:225381/1‑69 (MQ=255)
                  tATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGa                                       >  1:1931256/1‑69 (MQ=255)
                  tATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGa                                       >  1:740384/1‑69 (MQ=255)
                  tATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGa                                       >  1:3080301/1‑69 (MQ=255)
                  tATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGa                                       >  1:1534122/1‑69 (MQ=255)
                  tATTCTGGGCACCATAGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGa                                       >  1:3144924/1‑69 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:2142825/69‑1 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:2618271/69‑1 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:1739609/69‑1 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:1966639/69‑1 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:745309/69‑1 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:2192949/69‑1 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:1858191/69‑1 (MQ=255)
                   aTTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGAc                                      <  1:1881975/69‑1 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:422892/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:2173666/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:977436/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:3017182/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:3063008/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:835810/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:1450439/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:3245695/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:3281508/1‑69 (MQ=255)
                               aTCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCg                          >  1:1092159/1‑69 (MQ=255)
                                    tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                      <  1:816822/68‑1 (MQ=255)
                                    tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                      <  1:833367/68‑1 (MQ=255)
                                    tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                      <  1:2644965/68‑1 (MQ=255)
                                    tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                      <  1:1354021/68‑1 (MQ=255)
                                    tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                      <  1:976177/68‑1 (MQ=255)
                                    tGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGAttt                      <  1:2349836/68‑1 (MQ=255)
                                     ggCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                    <  1:463315/69‑1 (MQ=255)
                                     ggCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                    <  1:2142121/69‑1 (MQ=255)
                                     ggCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                    <  1:543207/69‑1 (MQ=255)
                                     ggCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                    <  1:2060123/69‑1 (MQ=255)
                                      gCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                    <  1:3347565/68‑1 (MQ=255)
                                      gCGATGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTGTACGAAGCGATTTTa                    <  1:1775896/68‑1 (MQ=255)
                                        gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                 >  1:58832/1‑69 (MQ=255)
                                        gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                 >  1:141223/1‑69 (MQ=255)
                                        gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                 >  1:3416323/1‑69 (MQ=255)
                                        gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                 >  1:167177/1‑69 (MQ=255)
                                        gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                 >  1:540286/1‑69 (MQ=255)
                                        gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTagag                 >  1:2622914/1‑69 (MQ=255)
                                        gATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTaga                  >  1:2358653/1‑68 (MQ=255)
                                          tGACACCATCTTTACTACCCCTGCTAACTGTTTCACCGTCAAAGAGCTg                                   >  1:195965/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCt                                    >  1:3063877/1‑48 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:683295/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:686820/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:741932/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:1054745/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:541548/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:870366/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:3411267/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:664050/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:962104/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:1642961/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:2056329/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:2107426/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:3342834/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:216567/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:1159966/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:1751675/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:2722062/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:2897518/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:1682244/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:2978166/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:3007790/1‑49 (MQ=37)
                                          tGACACCATCTTTACTACCCCTGCTAACGGTTTCACCGTCAAAGAGCTg                                   >  1:1026490/1‑49 (MQ=37)
                                           gACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg              <  1:9243/69‑1 (MQ=255)
                                           gACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg              <  1:1105570/69‑1 (MQ=255)
                                           gACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg              <  1:1753466/69‑1 (MQ=255)
                                            acacCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg              <  1:217935/68‑1 (MQ=255)
                                              acCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTc           <  1:178404/69‑1 (MQ=255)
                                                    tttACCACCCCTGCTAACGGTTTCACAGTCAAAGCCATGTACGAAGCGATTTTAGAGCTGTTCGAcc       >  1:997627/1‑67 (MQ=255)
                                                    tttACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTg              >  1:2633055/1‑60 (MQ=255)
                                                    tttACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGAcc       >  1:770009/1‑67 (MQ=255)
                                                    tttACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGAcc       >  1:1578213/1‑67 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGAGCAGGAg  <  1:435904/68‑1 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:1574575/68‑1 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:2132053/68‑1 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:227021/68‑1 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:2443505/68‑1 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:38618/68‑1 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:3132679/68‑1 (MQ=255)
                                                        ccaccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:3197044/68‑1 (MQ=255)
                                                         caccCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAg  <  1:670487/67‑1 (MQ=255)
                                                         |                                                                  
ACTGGGCAAAGCAGAAGGTATTCTGGGCACCATCGCTGGCGATGACACCATCTTTACCACCCCTGCTAACGGTTTCACAGTCAAAGACCTGTACGAAGCGATTTTAGAGCTGTTCGACCAGGAG  >  minE/2200326‑2200449

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