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 2,475,522 T→C 21.3% Y218Y (TAT→TAC)  pstS → phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,475,5220TC21.3% 134.6 / 27.9 98Y218Y (TAT→TAC) pstSphosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (30/47);  new base C (4/17);  total (34/64)
Fisher's exact test for biased strand distribution p-value = 1.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

TGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCTGATGGTA  >  minE/2475458‑2475586
                                                                |                                                                
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:1709731/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:166572/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:2881032/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:2864898/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:2445017/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:1510569/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:2850108/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:1465186/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:3308495/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:1396342/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:1370377/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:2839019/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:131615/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:1916582/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:3099747/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTg                                                              <  1:2123929/69‑1 (MQ=255)
tGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTACGTTg                                                              <  1:1319161/69‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:2145462/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:2280954/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:316822/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:2146859/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:1583567/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:481079/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:847088/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:1212328/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            <  1:2631956/67‑1 (MQ=255)
    cGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTCATGTTGaa                                                            <  1:2150386/67‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:2467858/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:2565729/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:3059204/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:279962/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:2778339/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:117398/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:1248015/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:3300957/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:1294299/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:1939051/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:1670798/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:1483066/68‑1 (MQ=255)
           ggTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTa                                                    <  1:1349367/68‑1 (MQ=255)
              aaCGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTAcgcg                                                <  1:306264/69‑1 (MQ=255)
              aaCGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTAcgcg                                                <  1:398009/69‑1 (MQ=255)
              aaCGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTAcgcg                                                <  1:2542974/69‑1 (MQ=255)
              aaCGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTAcgcg                                                <  1:822865/69‑1 (MQ=255)
               acgacgGTATCGCGGCGTTCGTTGAGCGTCTGCCGGGTGCATTTGGTTATGTTGaa                                                            <  1:2119322/56‑1 (MQ=255)
               acgacgGTATCGCCGCGTTCGTTCAGCGTCTTCCGGGTGCAATTGGTTATGTTGaa                                                            >  1:2768366/1‑56 (MQ=255)
               acgacgGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            >  1:2401484/1‑56 (MQ=255)
               acgacgGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            >  1:2996183/1‑56 (MQ=255)
               acgacgGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            >  1:326405/1‑56 (MQ=255)
               acgacgGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGaa                                                            >  1:3074074/1‑56 (MQ=255)
                     gTATCGGCGCGTTCGTTCCGCGTCTGCCGGGTGCAGTTGGTTACGTTGAATATGCTTACGCGAAGCAg                                          >  1:443167/1‑68 (MQ=255)
                     gTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTGAATATGCTTACGCGAAGCAg                                          >  1:988028/1‑68 (MQ=255)
                     gTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAGTTGGTTACGTTGAATATGCTTACGCGAAGCAg                                          >  1:2605853/1‑68 (MQ=255)
                     gTATCGCCGCGTTCGTTCAGCGTCTGCAGGGTGCAGTTGGTTACGTTGAATATGCTTACGCGAAGCAg                                          >  1:1132699/1‑68 (MQ=255)
                       aTCGCCGCGTTCGTTCAGCGTCTGCCGGGTGGAATTGGTTATGTTGaa                                                            >  1:3332115/1‑48 (MQ=255)
                       aTCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGa                                                             >  1:2077141/1‑47 (MQ=255)
                       aTCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaac                                       >  1:630804/1‑69 (MQ=255)
                       aTCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaac                                       >  1:2157330/1‑69 (MQ=255)
                       aTCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaac                                       >  1:1984592/1‑69 (MQ=255)
                       aTCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaac                                       >  1:203605/1‑69 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAata                                                          >  1:2893534/1‑47 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATTCt                                                      <  1:1314006/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:946724/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:540349/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:496917/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:493734/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:1404259/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:3368640/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:722279/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:2151564/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:2179484/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:1335981/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCt                                                      <  1:2367425/51‑1 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaacaac                                    >  1:2014121/1‑69 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaaca                                      >  1:3244349/1‑67 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaaca                                      >  1:739377/1‑67 (MQ=255)
                          gccgcGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaaca                                      >  1:3359347/1‑67 (MQ=255)
                          gccgcGATCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGaaca                                      >  1:440568/1‑67 (MQ=255)
                                                    tGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCg           >  1:2448054/1‑68 (MQ=255)
                                                    tGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCg           >  1:1701975/1‑68 (MQ=255)
                                                    tGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCg           >  1:3404763/1‑68 (MQ=255)
                                                    tGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCg           >  1:1583210/1‑68 (MQ=255)
                                                     gCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCt         <  1:3091916/69‑1 (MQ=255)
                                                     gCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCt         <  1:3095988/69‑1 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACTCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCTGATgg    >  1:416353/1‑68 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAtctc             >  1:739867/1‑59 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAtctc             >  1:64908/1‑59 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAtctc             >  1:996535/1‑59 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAtctc             >  1:2145629/1‑59 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAtctc             >  1:2912291/1‑59 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAtctc             >  1:2875709/1‑59 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAtctc             >  1:2841215/1‑59 (MQ=255)
                                                           ggTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGAt                >  1:2382901/1‑56 (MQ=255)
                                                             ttATTTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGATGATGGTa  <  1:2536201/68‑1 (MQ=255)
                                                             ttATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCTGATGGTa  <  1:1524872/68‑1 (MQ=255)
                                                             ttATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCTGATGGTa  <  1:2626450/68‑1 (MQ=255)
                                                             ttATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCTGATGGTa  <  1:880512/68‑1 (MQ=255)
                                                             ttATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCTGATGGTa  <  1:1206051/68‑1 (MQ=255)
                                                                |                                                                
TGGGCGGTAAAGGTAACGACGGTATCGCCGCGTTCGTTCAGCGTCTGCCGGGTGCAATTGGTTATGTTGAATATGCTTACGCGAAGCAGAACAACCTGGCGTACACCAAACTGATCTCCGCTGATGGTA  >  minE/2475458‑2475586

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