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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 965,844 A→T 83.8% V17D (GTT→GAT)  ydeM ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE965,8440AT83.8% 213.1 / 30.0 86V17D (GTT→GAT) ydeMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (8/6);  new base T (38/34);  total (46/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

AGAGTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTCGCTCAATAAGG  >  minE/965778‑965913
                                                                  |                                                                     
agagTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAtcac                                                                    <  1:91415/70‑1 (MQ=255)
  agTGCTGTCATCCATCCGTTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACAtt                                                                 <  1:387267/71‑1 (MQ=255)
  agTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATcaca                                                                   >  1:5499357/1‑69 (MQ=255)
  agTGCTGTCATCCATCCATTTTTAATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACAtt                                                                 >  1:4984403/1‑71 (MQ=255)
    tGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTT‑AAGGTAAAAACAGTAATCACATTTga                                                              <  1:4796408/71‑1 (MQ=255)
      cTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTgag                                                             <  1:4952136/71‑1 (MQ=255)
      cTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTga                                                              <  1:4921839/70‑1 (MQ=255)
         tCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTga                                                              <  1:515332/67‑1 (MQ=255)
         tCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTga                                                              <  1:2309148/67‑1 (MQ=255)
         tCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTga                                                              <  1:2300436/67‑1 (MQ=255)
         tCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGAt                                                           <  1:5388274/70‑1 (MQ=255)
         tCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGAt                                                           <  1:3634251/70‑1 (MQ=255)
           atccatccATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTa                                                         >  1:3100986/1‑70 (MQ=255)
           atccatccATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTa                                                         <  1:4842690/70‑1 (MQ=255)
             ccatccatTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACAt                                                      >  1:5110919/1‑71 (MQ=255)
               atccatTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTa                                                         <  1:3492584/66‑1 (MQ=255)
                 ccatTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTa                                                         <  1:5528483/64‑1 (MQ=255)
                  catTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACAttt                                                                >  1:3245571/1‑56 (MQ=255)
                  catTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaa                                                  <  1:650236/70‑1 (MQ=255)
                  catTTTTCATGAGTAAACTGCGACTCATTTTCAAGGTAAAAACAGTAATCACAttt                                                                >  1:3529734/1‑56 (MQ=39)
                    tttttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACAttt                                                                <  1:4198136/54‑1 (MQ=255)
                    tttttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACAt                                                                  <  1:2396778/52‑1 (MQ=255)
                    tttttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTg                                                               <  1:3870497/55‑1 (MQ=255)
                      tttCATGAGTAAACTGCGACTTTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTg                                             >  1:4356211/1‑71 (MQ=39)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTaaa                                                                       >  1:5009941/1‑45 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGAt                                                           >  1:2223786/1‑57 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaaaa                                                >  1:3439668/1‑68 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAAc                                               >  1:5171920/1‑69 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTAAATTGAAAACTg                                             >  1:3986780/1‑71 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTgaga                                                            >  1:1498619/1‑56 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTgag                                                             >  1:1013720/1‑55 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTgag                                                             >  1:2335833/1‑55 (MQ=255)
                      tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTAc                                                        >  1:1716406/1‑60 (MQ=255)
                        tCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTg                                             >  1:3080889/1‑69 (MQ=255)
                        tCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTgg                                            <  1:4028570/70‑1 (MQ=255)
                         cATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTgg                                            <  1:2707478/69‑1 (MQ=255)
                         cATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTg                                                               >  1:1963503/1‑50 (MQ=255)
                         cATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTg                                                               >  1:1199636/1‑50 (MQ=255)
                         cATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTg                                                               >  1:86428/1‑50 (MQ=255)
                          aTGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACAttt                                                                <  1:2670012/48‑1 (MQ=255)
                          aTGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAgg                                         <  1:5072238/71‑1 (MQ=255)
                           tGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAggg                                        <  1:1482876/71‑1 (MQ=255)
                              gTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACAt                                                      >  1:646930/1‑54 (MQ=255)
                              gTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCtt                                     <  1:246340/71‑1 (MQ=255)
                               tAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTa                                                         <  1:24997/50‑1 (MQ=255)
                                   cTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTga                                                              <  1:1973096/41‑1 (MQ=255)
                                   cTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTga                                                              <  1:4014642/41‑1 (MQ=255)
                                    tGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTg                                                    <  1:5653779/50‑1 (MQ=255)
                                    tGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTg                                                    <  1:452207/50‑1 (MQ=255)
                                    tGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTg                                >  1:931420/1‑70 (MQ=255)
                                      cGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTTAGATTACATTGaa                                                  >  1:3381366/1‑50 (MQ=25)
                                      cGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaa                                                  >  1:3538365/1‑50 (MQ=255)
                                      cGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaa                                                  >  1:4997373/1‑50 (MQ=255)
                                      cGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACt                                              <  1:721373/54‑1 (MQ=255)
                                      cGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACt                                              <  1:2171601/54‑1 (MQ=255)
                                         ctctTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTa                                                         >  1:4545080/1‑40 (MQ=255)
                                         ctctTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaaaa                                                >  1:4694771/1‑49 (MQ=255)
                                         ctctTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaaaa                                                >  1:3883818/1‑49 (MQ=255)
                                         ctctTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGt                          >  1:4282867/1‑71 (MQ=255)
                                         ctctTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGt                          >  1:3226067/1‑71 (MQ=255)
                                          tctTTTTCAATGTAAAAACAGTAATCACATTTGAGATTACATTGaa                                                  <  1:881176/46‑1 (MQ=37)
                                          tctTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGt                               <  1:3089325/65‑1 (MQ=255)
                                            tttttCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaaaa                                                >  1:4234491/1‑46 (MQ=255)
                                            tttttCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaaaa                                                >  1:2858938/1‑46 (MQ=255)
                                            tttttCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGc                                  <  1:1655884/60‑1 (MQ=255)
                                              tttCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaa                                                  >  1:3272981/1‑42 (MQ=255)
                                               ttCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCAt                      <  1:4736945/69‑1 (MQ=255)
                                                 cAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaaa                                                 >  1:4258970/1‑40 (MQ=255)
                                                 cAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCg                    >  1:685484/1‑69 (MQ=255)
                                                  aaGTTAATAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCt                  <  1:4332518/70‑1 (MQ=255)
                                                     gTAAAAACAGTAATCACATTTGAGATTACATTGAAAACt                                              >  1:551372/1‑39 (MQ=255)
                                                     gTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCa                       >  1:2550161/1‑62 (MQ=255)
                                                      tAAAAACAGTAATCACATTTGAGATTACATTGaaa                                                 <  1:1300204/35‑1 (MQ=255)
                                                      tAAAAACAGTAATCACATTTGAGATTACATTGaaa                                                 <  1:125606/35‑1 (MQ=255)
                                                       aaaaaCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTgg                                   >  1:604799/1‑48 (MQ=255)
                                                        aaaaCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCAt                      <  1:1006246/60‑1 (MQ=255)
                                                        aaaaCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCAt                      <  1:1417644/60‑1 (MQ=255)
                                                           aCAGTAATCACATTTGAGATTACATTGAAAACTGGa                                           >  1:5227133/1‑36 (MQ=255)
                                                           aCAGTAATCACATTTGAGATTACATTGAAAACTGGAg                                          >  1:1569186/1‑37 (MQ=255)
                                                           aCAGTAATCACATTTGAGATTACATTGAAAACTGGAg                                          >  1:3596215/1‑37 (MQ=255)
                                                           aCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAtct              >  1:4244173/1‑65 (MQ=255)
                                                           aCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAtct              >  1:5403224/1‑65 (MQ=255)
                                                           aCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAtct              >  1:5484103/1‑65 (MQ=255)
                                                           aCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAtct              >  1:1366776/1‑65 (MQ=255)
                                                            cAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAAc                            >  1:1309819/1‑50 (MQ=255)
                                                             aGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTCGCTCAAt      <  1:3497615/71‑1 (MQ=255)
                                                             aGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTCGCTCAAt      <  1:5089946/71‑1 (MQ=255)
                                                               tAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTCGCTCAAt      >  1:4935096/1‑69 (MQ=255)
                                                                 aaCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTCGCTCAATAAgg  >  1:5281260/1‑71 (MQ=255)
                                                                  |                                                                     
AGAGTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTCGCTCAATAAGG  >  minE/965778‑965913

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