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 2,048,393 T→A 57.4% I654I (ATA→ATT)  glnE ← fused deadenylyltransferase and adenylyltransferase for glutamine synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,048,3930TA57.4% 32.2 / 73.6 75I654I (ATA→ATT) glnEfused deadenylyltransferase and adenylyltransferase for glutamine synthetase
Reads supporting (aligned to +/- strand):  ref base T (7/25);  new base A (21/22);  total (28/47)
Fisher's exact test for biased strand distribution p-value = 2.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

TTCAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATC  >  minE/2048328‑2048461
                                                                 |                                                                    
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:920192/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:230055/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:2561774/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:2711222/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:2960682/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:3014913/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:3221935/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:1284164/68‑1 (MQ=255)
ttcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:3243515/68‑1 (MQ=255)
 tcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:1369453/67‑1 (MQ=255)
 tcAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTAt                                                                    <  1:1497143/67‑1 (MQ=255)
      tGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCt                                                             <  1:1796917/69‑1 (MQ=255)
      tGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCt                                                             <  1:1425484/69‑1 (MQ=255)
       gATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCt                                                             >  1:324944/1‑68 (MQ=255)
       gATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCt                                                             >  1:1520055/1‑68 (MQ=255)
                   cGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCgcc                                                       >  1:1899982/1‑62 (MQ=255)
                   cGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCgcc                                                       >  1:2257283/1‑62 (MQ=255)
                   cGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCgcc                                                       >  1:2285506/1‑62 (MQ=255)
                   cGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCgcc                                                       >  1:2589637/1‑62 (MQ=255)
                   cGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCgcc                                                       >  1:3417518/1‑62 (MQ=255)
                                 aTTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTc                                  <  1:1363158/69‑1 (MQ=255)
                                 aTTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTc                                  <  1:225619/69‑1 (MQ=255)
                                 aTTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTc                                  <  1:526614/69‑1 (MQ=255)
                                 aTTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTc                                  <  1:3030340/69‑1 (MQ=255)
                                 aTTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTc                                  <  1:798184/69‑1 (MQ=255)
                                          cACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTtcatc                         <  1:1211350/69‑1 (MQ=255)
                                          cACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTtcatc                         <  1:2677948/69‑1 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCCGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:1035152/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGt                   >  1:557717/1‑68 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGt                   >  1:2763407/1‑68 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:774058/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:54384/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:2667972/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:79342/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:3362151/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:707662/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:375993/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:3051575/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:3053368/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:1017763/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:2142928/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:161020/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:1106486/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:1795185/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:1145093/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:1486834/1‑69 (MQ=255)
                                                 gctgAACGACGGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTa                  >  1:1972423/1‑69 (MQ=255)
                                                 gctgAACGACGGCATAAATCATGGCTTCTgccagcc                                                   >  1:915682/1‑36 (MQ=25)
                                                       cgacgGCATCAATCATGGCTTCTGCCTGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:2046597/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTATGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:2186120/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGctt              <  1:828415/67‑3 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGctt              <  1:824536/67‑3 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1674021/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1003756/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:3312304/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1492154/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1408550/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1274165/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:736548/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:76363/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1096839/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:859703/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:880724/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:3115017/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:185212/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1963672/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:2177871/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:2564342/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:2856938/67‑1 (MQ=255)
                                                       cgacgGCATCAATCATGGCTTCTGCCAGCCAGGTTAAGTGATCGCTCACTTTCATTACCGGTAGCGt              <  1:1999568/67‑1 (MQ=255)
                                                             cATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGa      <  1:3063976/69‑1 (MQ=255)
                                                             cATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGa      <  1:2194756/69‑1 (MQ=255)
                                                             cATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGa      <  1:15399/69‑1 (MQ=255)
                                                             cATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGa      <  1:2834993/69‑1 (MQ=255)
                                                             cATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGa      <  1:778655/69‑1 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCATGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGatat   >  1:1645787/1‑68 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACtt                              >  1:2793191/1‑41 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:2826521/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:1994869/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:1049681/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:2744846/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:2830049/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:2034765/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:1365893/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:2885224/1‑69 (MQ=255)
                                                                 tATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATc  >  1:1729657/1‑69 (MQ=255)
                                                                 |                                                                    
TTCAGGTGATTCGGCTTACCGTAGCGGGCAACCATTTGAACCCACGCCTGCTGAACGACGGCATCTATCATGGCTTCCGCCAGCCAGGTTAAGTGATCGCTCACTTTCATCACCGGTAGCGTACCGGCGATATC  >  minE/2048328‑2048461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A