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 872,874 A→G 31.0% T22T (ACA→ACG)  cysB → DNA‑binding transcriptional dual regulator, O‑acetyl‑L‑serine‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE872,8740AG31.0% 105.6 / 59.9 119T22T (ACA→ACG) cysBDNA‑binding transcriptional dual regulator, O‑acetyl‑L‑serine‑binding
Reads supporting (aligned to +/- strand):  ref base A (52/30);  new base G (33/4);  total (85/34)
Fisher's exact test for biased strand distribution p-value = 4.11e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

Only 100 of 119 total aligned reads displayed.

TACAACAACTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACGAGCTA  >  minE/872816‑872940
                                                          |                                                                  
tACAACAACTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGAc                                                          >  1:301923/1‑69 (MQ=255)
    acaacTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTa                                                      <  1:2565599/69‑1 (MQ=255)
       acTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTacac                                                   >  1:2095565/1‑69 (MQ=255)
       acTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTacac                                                   >  1:2902379/1‑69 (MQ=255)
       acTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTacac                                                   >  1:380082/1‑69 (MQ=255)
       acTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTacac                                                   >  1:1412357/1‑69 (MQ=255)
       acTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTacac                                                   >  1:184537/1‑69 (MQ=255)
       acTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTacac                                                   >  1:2313384/1‑69 (MQ=255)
       acTTCGCTATATAGTAGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTaca                                                    >  1:357934/1‑68 (MQ=255)
             cTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATcac                                              <  1:2772919/68‑1 (MQ=255)
             cTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATcac                                              <  1:842848/68‑1 (MQ=255)
             cTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATcac                                              <  1:2214226/68‑1 (MQ=255)
                  ttgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCgg                                                                >  1:1924652/1‑45 (MQ=255)
                  ttgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAAccc                                         >  1:216331/1‑68 (MQ=255)
                  ttgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAAccc                                         >  1:528706/1‑68 (MQ=255)
                  ttgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAAccc                                         >  1:3092661/1‑68 (MQ=255)
                  ttgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAAccc                                         >  1:823923/1‑68 (MQ=255)
                  ttgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAAccc                                         >  1:1185937/1‑68 (MQ=255)
                  ttgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAAccc                                         >  1:3005277/1‑68 (MQ=255)
                   tgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCgg                                       >  1:938979/1‑69 (MQ=255)
                   tgttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCgg                                       >  1:196806/1‑69 (MQ=255)
                    gttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCggg                                      <  1:2595872/69‑1 (MQ=255)
                    gttgAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCggg                                      <  1:490828/69‑1 (MQ=255)
                          gtggtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACtt                                                        >  1:3323380/1‑45 (MQ=255)
                          gtggtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCTGGATc                                   >  1:1878050/1‑66 (MQ=255)
                          gtggtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAg                                 >  1:1535341/1‑68 (MQ=255)
                          gtggtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAg                                 >  1:1450903/1‑68 (MQ=255)
                          gtggtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAg                                 >  1:1416273/1‑68 (MQ=255)
                          gtggtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAg                                 >  1:901789/1‑68 (MQ=255)
                             gtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTaa                              >  1:1782501/1‑68 (MQ=255)
                             gtCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTaa                              >  1:718751/1‑68 (MQ=255)
                              gcAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCggg                                      <  1:2981212/58‑1 (MQ=255)
                                aaTCATAACCTGAATGTCTCATCAACAGCGGAAGGa                                                           >  1:1003158/1‑36 (MQ=255)
                                aaTCATAACCTGAATGTCTCATCAACAGCGGAAGGa                                                           >  1:239621/1‑36 (MQ=255)
                                aaTCATAACCTGAATGTCTCATCAACAGCGGAAGGa                                                           >  1:2469108/1‑36 (MQ=255)
                                aaTCATAACCTGAATGTCTCATCAACAGCGGAAGGa                                                           >  1:630253/1‑36 (MQ=255)
                                aaTCATAACCTGAATGTCTCATCAACAGCGGAAGGa                                                           >  1:650035/1‑36 (MQ=255)
                                aaTCATAACCTGAATGTCTCATCAACAGCGGAAGGa                                                           >  1:1539852/1‑36 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAAc                                           >  1:2708818/1‑51 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:3383787/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:2880913/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:2867346/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:2894023/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:1220775/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:1488474/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:1531173/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:2632408/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:3088013/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:2528581/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:1609141/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:246656/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:2456867/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:692226/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:1702670/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:1738874/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:2204022/1‑68 (MQ=255)
                                 aTCATAACCTGAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:3335541/1‑68 (MQ=255)
                                 aTCATAACCCTAATGTCTCATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACaa                          >  1:1581657/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATGAACGGCGGAAGGACTTTa                                                      >  1:1419579/1‑37 (MQ=37)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:3018169/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:106375/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:326735/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:1610127/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:1873853/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:2720464/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:2069884/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:2585188/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACGGCGGAAGGACTTTa                                                      >  1:2097086/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTa                                                      >  1:867835/1‑37 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTa                                                      <  1:3341855/37‑1 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:827699/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:803107/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:981878/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:2280229/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:274757/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:2740233/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:3226943/1‑68 (MQ=255)
                                    aTAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTc                       >  1:2720987/1‑68 (MQ=255)
                                      aaCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:3278794/68‑1 (MQ=255)
                                      aaCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:1680410/68‑1 (MQ=255)
                                      aaCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:1911561/68‑1 (MQ=255)
                                      aaCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:1947356/68‑1 (MQ=255)
                                      aaCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:398881/68‑1 (MQ=255)
                                      aaCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:2377606/68‑1 (MQ=255)
                                      aaCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:1074052/68‑1 (MQ=255)
                                       aCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:8936/67‑1 (MQ=255)
                                       aCCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAg                     <  1:2863042/67‑1 (MQ=255)
                                                tctcATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAg          <  1:2989137/69‑1 (MQ=255)
                                                tctcATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAg          <  1:124198/69‑1 (MQ=255)
                                                tctcATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAg          <  1:71434/69‑1 (MQ=255)
                                                tctcATCAACGGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAg          <  1:2152186/69‑1 (MQ=255)
                                                      caACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACg       <  1:987308/66‑1 (MQ=255)
                                                      caACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACg       <  1:1873515/66‑1 (MQ=255)
                                                      caACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACg       <  1:2116939/66‑1 (MQ=255)
                                                      caACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACg       <  1:3273514/66‑1 (MQ=255)
                                                      caACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACg       <  1:2640888/66‑1 (MQ=255)
                                                       aaCAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACGAGCt   >  1:395945/1‑69 (MQ=255)
                                                         cAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACGAGCTa  <  1:1551379/68‑1 (MQ=255)
                                                         cAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACGAGCTa  <  1:1358554/68‑1 (MQ=255)
                                                         cAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACGAGCTa  <  1:2257792/68‑1 (MQ=255)
                                                          |                                                                  
TACAACAACTTCGCTATATTGTTGAGGTGGTCAATCATAACCTGAATGTCTCATCAACAGCGGAAGGACTTTACACATCACAACCCGGGATCAGTAAACAAGTCAGAATGCTGGAAGACGAGCTA  >  minE/872816‑872940

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