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 1,743,369 C→T 32.4% S88S (AGC→AGT)  nadB → quinolinate synthase, L‑aspartate oxidase (B protein) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,743,3690CT32.4% 72.0 / 40.7 83S88S (AGC→AGT) nadBquinolinate synthase, L‑aspartate oxidase (B protein) subunit
Reads supporting (aligned to +/- strand):  ref base C (19/37);  new base T (6/21);  total (25/58)
Fisher's exact test for biased strand distribution p-value = 3.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

ATGTGGAAGACACATTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGTTTGATACC  >  minE/1743302‑1743423
                                                                   |                                                      
aTGTGGAAGACACATTGATTGCTGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGc                                                        <  1:3048386/68‑1 (MQ=255)
aTGTGGAAGACACATTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGc                                                        <  1:2133953/68‑1 (MQ=255)
aTGTGGAAGACACATTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGc                                                        <  1:2603785/68‑1 (MQ=255)
aTGTGGAAGACACATTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGc                                                        <  1:1754064/68‑1 (MQ=255)
aTGTGGAAGACACATTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGc                                                        <  1:1292159/68‑1 (MQ=255)
aTGTGGAAGACACATTGATTGCAGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGc                                                        <  1:484090/68‑1 (MQ=255)
           acaTTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGATcc                                            >  1:2853277/1‑69 (MQ=255)
           acaTTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGATcc                                            >  1:1074688/1‑69 (MQ=255)
           acaTTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGATcc                                            >  1:2491322/1‑69 (MQ=255)
           acaTTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGATcc                                            >  1:1557873/1‑69 (MQ=255)
           acaTTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGATcc                                            >  1:1372442/1‑69 (MQ=255)
           acaTTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGATcc                                            >  1:3238351/1‑69 (MQ=255)
            caTTGATT‑CCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2683926/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:696888/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:3111693/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:325412/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:1978461/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2223361/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2646621/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:1926925/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:800951/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2419854/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:41262/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:563348/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:856474/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2482243/69‑1 (MQ=255)
             attgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATACtg                                          <  1:2852449/69‑1 (MQ=255)
              tttattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2544374/65‑1 (MQ=255)
              ttgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2131186/68‑1 (MQ=255)
              ttgattgCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:3045512/68‑1 (MQ=255)
                  ttgGCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2195749/64‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCTCCAGTAATGCACGa                                               <  1:1634915/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:1024313/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:3132306/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:265844/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:2953254/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:368913/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:194401/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:892200/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:830219/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:761906/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:697220/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:1530293/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:158073/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:1753702/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:3270603/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:1976947/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:2022598/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:3327502/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:3310981/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:2426209/52‑1 (MQ=255)
                         ggCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGTAATGCACGa                                               <  1:3302875/52‑1 (MQ=255)
                                aTTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          <  1:2976090/50‑1 (MQ=255)
                                aTTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGAc                       <  1:2606654/69‑1 (MQ=255)
                                aTTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGAc                       <  1:1744910/69‑1 (MQ=255)
                                aTTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGAc                       <  1:2547012/69‑1 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtgt                                         >  1:2877533/1‑50 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtgt                                         >  1:1072149/1‑50 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtgt                                         >  1:1188853/1‑50 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtgt                                         >  1:2430096/1‑50 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtgt                                         >  1:2701474/1‑50 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtgt                                         >  1:2831463/1‑50 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCtg                                          >  1:2663332/1‑49 (MQ=255)
                                 tttGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGAc                       <  1:1318978/68‑1 (MQ=255)
                                     cGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAgg                   <  1:117993/68‑1 (MQ=255)
                                     cGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAgg                   <  1:2439739/68‑1 (MQ=255)
                                      gATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggg                  <  1:3212265/68‑1 (MQ=255)
                                      gATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggg                  <  1:2887503/68‑1 (MQ=255)
                                      gATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggg                  <  1:1534641/68‑1 (MQ=255)
                                      gATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggg                  <  1:513036/68‑1 (MQ=255)
                                      gATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggg                  <  1:3346490/68‑1 (MQ=255)
                                      gATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggg                  <  1:2470133/68‑1 (MQ=255)
                                      gATCGCCATGCAGTTGAATTTGACGCCAGCAATGCACGATGCTGTGTGCAATGGCTAATCGACCAggg                  <  1:123767/68‑1 (MQ=255)
                                       aTCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggggg                <  1:755937/69‑1 (MQ=255)
                                           ccATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAggg                  <  1:2465910/63‑1 (MQ=255)
                                                cAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGc                                     >  1:2152728/1‑39 (MQ=255)
                                                cAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGc                                     >  1:1499509/1‑39 (MQ=255)
                                                cAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGc                                     >  1:70214/1‑39 (MQ=255)
                                                     gAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGTTTGATAcc  <  1:3276359/69‑1 (MQ=255)
                                                     gAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGAGGGTGTTGTTTGATAcc  <  1:818803/69‑1 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTgttttt         >  1:275528/1‑57 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:2533260/1‑58 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:2242859/1‑58 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:609184/1‑58 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:1680788/1‑58 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:2290642/1‑58 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:17087/1‑58 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:2830839/1‑58 (MQ=255)
                                                          tGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGttt        >  1:3325014/1‑58 (MQ=255)
                                                                   |                                                      
ATGTGGAAGACACATTGATTGCCGGGGCTGGTATTTGCGATCGCCATGCAGTTGAATTTGTCGCCAGCAATGCACGATCCTGTGTGCAATGGCTAATCGACCAGGGGGTGTTGTTTGATACC  >  minE/1743302‑1743423

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