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
A3 F2 I1 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 Exported 705,295 A→G 65.3% G32G (GGT→GGC)  ymcB ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported705,2950AG65.3% 101.0 / 84.1 98G32G (GGT→GGC) ymcBconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (12/22);  new base G (35/29);  total (47/51)
Fisher's exact test for biased strand distribution p-value = 8.97e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

GTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGC  >  Exported/705231‑705359
                                                                |                                                                
gTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAgg                                                             >  1:2467759/1‑70 (MQ=255)
gTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAgg                                                             >  1:1323517/1‑70 (MQ=255)
 ttGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGcc                                                                <  1:4646164/66‑1 (MQ=255)
   gCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAgg                                                             >  1:2067206/1‑67 (MQ=255)
    cGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGAt                                                        <  1:3325474/71‑1 (MQ=255)
    cGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGAt                                                        <  1:5082063/71‑1 (MQ=255)
     ggTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGa                                                         >  1:3525173/1‑69 (MQ=255)
      gTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATa                                                       >  1:1706304/1‑70 (MQ=255)
       ttGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATaaa                                                     >  1:5593110/1‑71 (MQ=255)
       ttGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATaaa                                                     <  1:2062256/71‑1 (MQ=255)
        tgtgTCACCAACTGGAGAACATTTTCCACGGGGCCAAAGGAAAGTGTCTGTTGTTCACCAGGCAGATaaa                                                     <  1:5455278/70‑1 (MQ=255)
        tgtgTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATaaa                                                     >  1:2814589/1‑70 (MQ=255)
         gtgtCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATaaa                                                     >  1:4949900/1‑69 (MQ=255)
           gtCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGt                                                 >  1:2948676/1‑71 (MQ=255)
              aCCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGt                                                 >  1:2400943/1‑68 (MQ=255)
              aCCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCAc                                              >  1:1826013/1‑71 (MQ=255)
              aCCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCAcc                                                                >  1:1668538/1‑53 (MQ=255)
                   cTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGAt                                                        <  1:5049762/56‑1 (MQ=255)
                   cTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTc                                         <  1:3369428/71‑1 (MQ=255)
                      gACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCtt                                      >  1:3873449/1‑71 (MQ=255)
                      gACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCtt                                      >  1:5235950/1‑71 (MQ=255)
                      gACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCt                                       <  1:5546400/70‑1 (MQ=255)
                      gACAACATTTTCCACGGGGCCAACGGAAAGTGTCTCTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCt                                       <  1:4351207/70‑1 (MQ=255)
                        caacaTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTc                                                <  1:5399677/59‑1 (MQ=255)
                         aacaTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTgcg                                   >  1:2601331/1‑71 (MQ=255)
                         aacaTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTgcg                                   >  1:4078041/1‑71 (MQ=255)
                           caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 <  1:3530549/71‑1 (MQ=255)
                           caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 <  1:2955657/71‑1 (MQ=255)
                           caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCAc                                                                 >  1:3232478/1‑39 (MQ=255)
                           caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 <  1:4272377/71‑1 (MQ=255)
                           caTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 <  1:3088228/71‑1 (MQ=255)
                            aTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCaa                                <  1:1279392/71‑1 (MQ=255)
                            aTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 >  1:335286/1‑70 (MQ=255)
                             ttttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATa                                                   >  1:1830588/1‑51 (MQ=255)
                             ttttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATa                                                   >  1:3971430/1‑51 (MQ=255)
                             ttttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATa                                                   >  1:4354141/1‑51 (MQ=255)
                             ttttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCaaa                               <  1:1024238/71‑1 (MQ=255)
                             ttttCCACGGGGCCAACGCAAAGTGTCTGTTGTTCGCCAGGCAGATAAATa                                                   >  1:3409565/1‑51 (MQ=255)
                              tttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCaaa                               <  1:45473/70‑1 (MQ=255)
                               ttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCa                                                               >  1:560286/1‑37 (MQ=255)
                               ttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTgcg                                   <  1:2325207/65‑1 (MQ=255)
                                 ccACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGc                            <  1:5039818/70‑1 (MQ=255)
                                  cACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGc                            <  1:1825760/69‑1 (MQ=255)
                                  cACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGc                            <  1:777315/69‑1 (MQ=255)
                                  cACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCAt                          <  1:890948/71‑1 (MQ=255)
                                   aCGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 <  1:248241/63‑1 (MQ=255)
                                    cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAATGCATgg                        <  1:740320/71‑1 (MQ=255)
                                    cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATgg                        <  1:470969/71‑1 (MQ=255)
                                    cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATgg                        <  1:5680/71‑1 (MQ=255)
                                    cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATgg                        <  1:3560483/71‑1 (MQ=255)
                                    cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATgg                        <  1:1854651/71‑1 (MQ=255)
                                    cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATgg                        <  1:2727676/71‑1 (MQ=255)
                                    cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATgg                        <  1:2969537/71‑1 (MQ=255)
                                     ggggCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATggg                       <  1:215805/71‑1 (MQ=255)
                                         ccAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGgtgt                   <  1:4442702/71‑1 (MQ=255)
                                           aaCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCa                 >  1:3774361/1‑71 (MQ=255)
                                           aaCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCa                 <  1:5450323/71‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCa                 >  1:451548/1‑70 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCa                 >  1:1364887/1‑70 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCAt                >  1:189995/1‑71 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCAt                <  1:3336826/71‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCAt                <  1:2637877/71‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTTACCGTTCCTTGCGCAAAGGCATGGGGTGTCAt                <  1:2653506/71‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa                           <  1:286123/60‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa                           <  1:4752110/60‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa                           <  1:5085695/60‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa                           <  1:3077881/60‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCa                           <  1:702857/60‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCAt                <  1:1454744/71‑1 (MQ=255)
                                            aCGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCAt                >  1:5073611/1‑71 (MQ=255)
                                             cGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTcc                                        >  1:2001150/1‑46 (MQ=255)
                                             cGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTcc                                        >  1:4677834/1‑46 (MQ=255)
                                              ggAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAg                                                  >  1:465907/1‑35 (MQ=255)
                                                aaaGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCa                 >  1:3802822/1‑66 (MQ=255)
                                                aaaGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACg            <  1:580404/71‑1 (MQ=255)
                                                  aGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTa          <  1:4032273/71‑1 (MQ=255)
                                                   gtgtCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCAtt               <  1:3854563/65‑1 (MQ=255)
                                                     gtCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAg                              >  1:3592397/1‑48 (MQ=255)
                                                      tCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAg       <  1:5053415/70‑1 (MQ=255)
                                                        tgttgtTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCaaa                               >  1:3158827/1‑44 (MQ=255)
                                                        tgttgtTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCaaa                               >  1:640365/1‑44 (MQ=255)
                                                        tgttgtTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 >  1:4782307/1‑42 (MQ=255)
                                                        tgttgtTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTaaa        >  1:5037737/1‑67 (MQ=255)
                                                        tgttgtTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTaaa        >  1:4238258/1‑67 (MQ=255)
                                                          ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATgggg                      >  1:3426767/1‑51 (MQ=255)
                                                          ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGgtg                    >  1:4623417/1‑53 (MQ=255)
                                                          ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGgtg                    >  1:4350422/1‑53 (MQ=255)
                                                          ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGgtg                    >  1:3420302/1‑53 (MQ=255)
                                                          ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTaa         <  1:1570900/64‑1 (MQ=255)
                                                          ttgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTaa         <  1:3507836/64‑1 (MQ=255)
                                                          ttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 <  1:2664524/40‑1 (MQ=255)
                                                          ttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCa                                 <  1:462931/40‑1 (MQ=255)
                                                          ttgttCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGc  >  1:1222528/1‑71 (MQ=255)
                                                           tgttCACCAGGCAGATAAATAGTCACCGATCCTTgc                                    >  1:541104/1‑36 (MQ=255)
                                                             ttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTc                  <  1:261186/52‑1 (MQ=255)
                                                             ttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTaaa        >  1:1754968/1‑62 (MQ=255)
                                                               cACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCAt                          >  1:3565230/1‑42 (MQ=255)
                                                               cACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCAt                          >  1:3119351/1‑42 (MQ=255)
                                                                |                                                                
GTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCACCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGC  >  Exported/705231‑705359

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