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 2,103,159 T→C 31.2% T198T (ACA→ACG)  agaR ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,103,1590TC31.2% 143.7 / 82.4 160T198T (ACA→ACG) agaRDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base T (57/53);  new base C (20/30);  total (77/83)
Fisher's exact test for biased strand distribution p-value = 1.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 160 total aligned reads displayed.

CACGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAATT  >  minE/2103096‑2103224
                                                               |                                                                 
cACGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCt                                                              <  1:1824745/69‑1 (MQ=255)
cACGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCt                                                              <  1:1636383/69‑1 (MQ=255)
 aCGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCt                                                              <  1:237807/68‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:862318/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:2785714/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:2228283/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:2192808/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:2080674/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:1265679/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:1522510/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:601994/69‑1 (MQ=255)
  cGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:1357133/69‑1 (MQ=255)
               cGCAACTTCGCACTTCCGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGa                                                            <  1:1315093/56‑1 (MQ=255)
                      tCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAgatcgat                                         >  1:361340/1‑68 (MQ=255)
                      tCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAgatcgat                                         >  1:1600727/1‑68 (MQ=255)
                        atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:2241559/66‑1 (MQ=255)
                        atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:177892/66‑1 (MQ=255)
                        atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:373298/66‑1 (MQ=255)
                        atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:1863140/66‑1 (MQ=255)
                        atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:596629/66‑1 (MQ=255)
                         cacaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGatcgatcg                                       <  1:1572798/67‑1 (MQ=255)
                         cacaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGatcgatcg                                       <  1:1150547/67‑1 (MQ=255)
                           caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:1573585/1‑47 (MQ=255)
                           caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:1026456/1‑47 (MQ=255)
                           caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:1384921/1‑47 (MQ=255)
                           caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:25481/1‑47 (MQ=255)
                           caTCCGA‑GGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:2406546/1‑46 (MQ=39)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGat                                                           >  1:318577/1‑40 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCa                                                >  1:1072151/1‑52 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:1080344/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3259067/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3332994/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3197591/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3089891/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:2346141/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:2460784/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:2572461/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:695217/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:1372482/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:1375257/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:496859/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3377850/1‑53 (MQ=37)
                               cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:720468/1‑53 (MQ=37)
                               cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:23350/1‑68 (MQ=255)
                               cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:681932/1‑68 (MQ=255)
                               cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:3206967/1‑68 (MQ=255)
                               cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:641552/1‑68 (MQ=255)
                                   ggTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:1459222/58‑1 (MQ=255)
                                     tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:1052667/69‑1 (MQ=255)
                                     tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:3356325/69‑1 (MQ=255)
                                     tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:3311860/69‑1 (MQ=255)
                                     tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:3341766/69‑1 (MQ=255)
                                     tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:2682094/69‑1 (MQ=255)
                                      ttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:2661737/68‑1 (MQ=255)
                                       tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:1007121/69‑1 (MQ=255)
                                       tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:842724/69‑1 (MQ=255)
                                       tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:2310351/69‑1 (MQ=255)
                                       tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:135974/69‑1 (MQ=255)
                                          aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1142688/68‑1 (MQ=255)
                                          aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1662008/68‑1 (MQ=255)
                                          aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1665351/68‑1 (MQ=255)
                                          aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1959235/68‑1 (MQ=255)
                                          aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:3291636/68‑1 (MQ=255)
                                           cGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAg                    <  1:2807827/68‑1 (MQ=255)
                                           cGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGc                   <  1:2205522/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:975683/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:1024027/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:773543/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:672676/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:659086/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:574426/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:1634288/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:2183564/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:3049416/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:2817396/69‑1 (MQ=255)
                                            gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:290084/69‑1 (MQ=255)
                                               cttcatcttcatTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:2913158/63‑1 (MQ=255)
                                                 tcatcttcatTATGTGTGCTGACGCCGCGCTCCAgatcga                                          >  1:1135740/1‑40 (MQ=255)
                                                 tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:464697/1‑64 (MQ=255)
                                                 tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:1279784/1‑64 (MQ=255)
                                                 tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:2970636/1‑64 (MQ=255)
                                                 tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:1550744/1‑64 (MQ=255)
                                                 tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:229335/1‑64 (MQ=255)
                                                 tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:1736218/1‑64 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:1267048/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:582932/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2422890/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2675829/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:100531/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2514623/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2146767/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:512596/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:459463/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2261827/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:1784555/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:1840664/1‑42 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGt         >  1:448509/1‑68 (MQ=255)
                                                      ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGt         >  1:846957/1‑68 (MQ=255)
                                                            aTGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAAtt  >  1:479114/1‑69 (MQ=255)
                                                            aTGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAAtt  >  1:1940604/1‑69 (MQ=255)
                                                               |                                                                 
CACGATGATCCGTTCCGCAACTTCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAATT  >  minE/2103096‑2103224

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