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 1,528,832 T→A 51.9% F606Y (TTT→TAT)  trmC → fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,528,8320TA51.9% 1.9 / 91.3 77F606Y (TTT→TAT) trmCfused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme
Reads supporting (aligned to +/- strand):  ref base T (19/18);  new base A (18/22);  total (37/40)
Fisher's exact test for biased strand distribution p-value = 6.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

AACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCTGTGTG  >  minE/1528770‑1528894
                                                              |                                                              
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACg                                                           >  1:2617552/2‑68 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:3185257/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:2387709/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:2404594/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:2109277/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:253670/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:2669450/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:1910005/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:2881515/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:2938930/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:3074853/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:33363/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:1002584/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:1030685/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:925375/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:142136/2‑69 (MQ=255)
tacacTCGTGGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGa                                                          >  1:60663/2‑69 (MQ=255)
tacacTCGTCGAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACg                                                           >  1:2768968/2‑68 (MQ=255)
 acacTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGa                                                          >  1:1450029/1‑68 (MQ=255)
 acacTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGa                                                          >  1:1925047/1‑68 (MQ=255)
 acacTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGAt                                                         >  1:1190555/1‑69 (MQ=255)
 acacTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGAt                                                         >  1:133425/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATctct                                                     >  1:28483/1‑68 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:587700/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:2453372/69‑1 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:2457217/69‑1 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:452346/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:2888256/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:574527/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:101151/69‑1 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:3273257/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:544083/69‑1 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:388413/69‑1 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:2038848/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:1470255/69‑1 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:1803519/69‑1 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:1872300/1‑69 (MQ=255)
      cGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    >  1:1563473/1‑69 (MQ=255)
       gTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:2820441/68‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:3234009/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:3201118/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:1660701/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:1654586/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:161139/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:177720/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:362710/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:2822454/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:369607/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:2748182/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:154134/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:2670233/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:1517733/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:1980522/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:255300/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:1983571/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:2469330/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:743360/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:826959/69‑1 (MQ=255)
          gAATATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:881877/69‑1 (MQ=255)
           aaTATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:2280702/68‑1 (MQ=255)
           aaTATGCGTCGCTGGCGGAGAAGAAAGATGAAGCGGTAAGCGCGCCGGTTTATGACGATCTCTTTATg                                                <  1:2125768/68‑1 (MQ=255)
               tGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTg                                            >  1:849960/1‑68 (MQ=255)
               tGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTg                                            >  1:2729682/1‑68 (MQ=255)
               tGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTg                                            >  1:1358345/1‑68 (MQ=255)
                 cgtcgtTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCgg                                         >  1:849133/1‑69 (MQ=255)
                     gtTGGCGGAGCAGAAAGATGAGGCGGTATGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCttt                                     >  1:2722848/1‑69 (MQ=255)
                     gtTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCttt                                     >  1:999579/1‑69 (MQ=255)
                          cGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCtt                                                    <  1:1667721/49‑1 (MQ=255)
                                  aaaGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTGTTTATGTTTGCGGCTTTAGGTTCTCGCGGt                        <  1:3418086/69‑1 (MQ=255)
                                  aaaGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGt                        <  1:1353504/69‑1 (MQ=255)
                                  aaaGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGt                        <  1:636341/69‑1 (MQ=255)
                                        gAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTgtgt                  <  1:1916846/69‑1 (MQ=255)
                                        gAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTgtgt                  <  1:1804118/69‑1 (MQ=255)
                                        gAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTgtgt                  <  1:2351357/69‑1 (MQ=255)
                                        gAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTgtgt                  <  1:1277295/69‑1 (MQ=255)
                                        gAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTgtgt                  <  1:3103197/69‑1 (MQ=255)
                                                    gcgcCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCtg      <  1:2507968/69‑1 (MQ=255)
                                                            ttttGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCtgtgtg  >  1:1934519/1‑65 (MQ=255)
                                                            ttttGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCtgtgtg  >  1:606131/1‑65 (MQ=255)
                                                            ttttGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCtgtgtg  >  1:2151552/1‑65 (MQ=255)
                                                            ttttGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTATGccc           >  1:606362/1‑56 (MQ=255)
                                                              |                                                              
AACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCTGTGTG  >  minE/1528770‑1528894

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