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 1,259,850 C→T 16.5% Q358Q (CAG→CAA)  torZ ← trimethylamine N‑oxide reductase system III, catalytic subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,259,8500CT16.5% 212.1 / 29.6 91Q358Q (CAG→CAA) torZtrimethylamine N‑oxide reductase system III, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base C (44/32);  new base T (8/7);  total (52/39)
Fisher's exact test for biased strand distribution p-value = 7.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

CGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGAC  >  minE/1259781‑1259918
                                                                     |                                                                    
cGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGGATCCAGTGTTTCTGTTCACCATATTGCt                                                                     <  1:3908737/71‑1 (MQ=255)
   tgtACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGgc                                                                  >  1:2667483/1‑71 (MQ=255)
           tttGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCAt                                                           >  1:1989388/3‑70 (MQ=255)
           tttGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCAt                                                           >  1:4054543/3‑70 (MQ=255)
           tCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCt                                                                     <  1:148507/60‑1 (MQ=255)
            cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc                                                         >  1:4127653/1‑71 (MQ=255)
            cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc                                                         >  1:3686733/1‑71 (MQ=255)
            cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc                                                         >  1:761480/1‑71 (MQ=255)
             tGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcc                                                        >  1:5063077/1‑71 (MQ=255)
               cccTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcccc                                                      <  1:2038243/71‑1 (MQ=255)
               cccTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcccc                                                      <  1:4124712/71‑1 (MQ=255)
                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTccc                                                       >  1:175182/4‑69 (MQ=255)
                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTccc                                                       >  1:5694394/4‑69 (MQ=255)
                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTccc                                                       >  1:1510680/4‑69 (MQ=255)
                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCAACAAACTGTTGGCGCTGCATTCCCCa                                                     <  1:5584119/68‑1 (MQ=255)
                ccTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcccc                                                      <  1:3988489/70‑1 (MQ=255)
                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCt                                                               <  1:1665276/59‑1 (MQ=255)
                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTccc                                                       >  1:3949943/1‑67 (MQ=255)
                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGc                                                   >  1:3334757/1‑71 (MQ=255)
                   aaCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGcc                                                  >  1:1835596/1‑71 (MQ=255)
                    aCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTgg                                                                   >  1:205362/1‑53 (MQ=255)
                    aCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTgg                                                                   >  1:4864383/1‑53 (MQ=255)
                     cATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTg                                                >  1:2768747/1‑71 (MQ=255)
                      aTCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGc                                               <  1:5090975/71‑1 (MQ=255)
                         gctgccAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTCCCCAGCCTGCCAt                                            >  1:2796622/4‑71 (MQ=255)
                         gccgccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCa                                                     >  1:3956571/1‑62 (MQ=255)
                          ctgccAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTCCCCAGCCTGCCATc                                           <  1:1108008/69‑1 (MQ=255)
                          ccgccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATc                                           <  1:4935187/71‑1 (MQ=255)
                           tgccAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTc                                                         <  1:4673168/55‑1 (MQ=255)
                            gccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGc                                               >  1:4741654/1‑65 (MQ=255)
                            gccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGc                                               >  1:2199633/1‑65 (MQ=255)
                            gccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAg                                         <  1:2306961/71‑1 (MQ=255)
                            gccAGCGTCACCAGCATCCAGTGTTTCTGTTAACCATATTGCTGGCGCTGAATTCCCCAGCCTGc                                               >  1:100003/1‑65 (MQ=255)
                               aGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCAt                                            >  1:557917/1‑65 (MQ=255)
                               aGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCAt                                            >  1:3026975/1‑65 (MQ=255)
                                gCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAg                                         <  1:4246466/67‑1 (MQ=255)
                                 cGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATtg                                    <  1:3602227/71‑1 (MQ=255)
                                    cACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATtgtg                                  >  1:88160/1‑70 (MQ=255)
                                     aCCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGc                                 >  1:5606113/1‑70 (MQ=255)
                                      ccAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGa                               <  1:1211039/71‑1 (MQ=255)
                                       cAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGAt                              >  1:4539136/1‑71 (MQ=255)
                                       cAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGAt                              >  1:97902/1‑71 (MQ=255)
                                       cAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGAt                              >  1:2999096/1‑71 (MQ=255)
                                        aGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGAtt                             <  1:5489981/71‑1 (MQ=255)
                                           aTCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTcg                           <  1:5386591/70‑1 (MQ=255)
                                            tCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGAt                              <  1:5036926/66‑1 (MQ=255)
                                              cAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTcgccg                        <  1:3492910/70‑1 (MQ=255)
                                               aGTGTTTCTGTTCACCATATTGCTGCCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTcgccgc                       >  1:2695104/1‑70 (MQ=255)
                                                gtgtTTCTGTTCACCATATTGCTGGCGCTGAATTcc                                                        <  1:4637152/36‑1 (MQ=255)
                                                gtgtTTCTGTTCACCATATTGCTGGCGCTGAATTcc                                                        <  1:510371/36‑1 (MQ=255)
                                                gtgtTTCTGTTCACCATATTGCTGGCGCTGAATTcc                                                        <  1:1023609/36‑1 (MQ=255)
                                                  gtTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCa                                       >  1:4169970/1‑51 (MQ=255)
                                                   ttttTGCTCACCAAACTGTTGGGGCTGCATTCCCCAGCCTGCCATCa                                          <  1:3389962/47‑1 (MQ=16)
                                                   ttttTGCTCACCAAACTGTTGGCGCTGCATTCCCCAGCCTGCCATCa                                          <  1:2860386/47‑1 (MQ=19)
                                                   ttttTGCTCACCAAACTGTTGGCGCTGCATTCCCCAGCCTGCCATCa                                          <  1:5131128/47‑1 (MQ=19)
                                                   ttttTGCTCACCAAACTGTTGGCGCTGCATTCCCCAGCCTGCCATCa                                          <  1:3626513/47‑1 (MQ=19)
                                                   tttCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCAt                    >  1:3645741/1‑69 (MQ=255)
                                                    ttCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCAt                                            >  1:4300713/1‑44 (MQ=255)
                                                     tCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCa                                             >  1:5561233/1‑42 (MQ=255)
                                                     tCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCa                                             >  1:3307494/1‑42 (MQ=255)
                                                     tCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCa                                             >  1:3588402/1‑42 (MQ=255)
                                                     tCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCa                                             >  1:407781/1‑42 (MQ=255)
                                                     tCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATtg                                    >  1:937116/1‑51 (MQ=255)
                                                     tCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGt                >  1:1023915/1‑71 (MQ=255)
                                                      cTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGt                <  1:325743/70‑1 (MQ=255)
                                                      cTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGt                <  1:4283614/70‑1 (MQ=255)
                                                       tGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGAtt                             >  1:5607194/1‑56 (MQ=255)
                                                       tGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGtt               >  1:3734576/1‑70 (MQ=255)
                                                         ttCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGc                                 <  1:4983520/50‑1 (MQ=255)
                                                         ttCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAg            >  1:5009449/1‑71 (MQ=255)
                                                           cACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGa                               >  1:4488154/1‑50 (MQ=255)
                                                           cACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGc           >  1:4959383/1‑70 (MQ=255)
                                                            aCCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGc                                 <  1:4316482/47‑1 (MQ=255)
                                                            aCCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGa         <  1:715806/71‑1 (MQ=255)
                                                            aCCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGa         <  1:5435687/71‑1 (MQ=255)
                                                              cATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGt       <  1:4070365/71‑1 (MQ=255)
                                                               atatTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATc                   <  1:3064520/58‑1 (MQ=255)
                                                               atatTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGtt      <  1:3701137/71‑1 (MQ=255)
                                                                tatTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGttt     <  1:2363911/71‑1 (MQ=255)
                                                                tatTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGttt     <  1:2157096/71‑1 (MQ=255)
                                                                tatTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGttt     <  1:706586/71‑1 (MQ=255)
                                                                tatTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGttt     >  1:1869497/1‑71 (MQ=255)
                                                                tatTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGttt     <  1:3416060/71‑1 (MQ=255)
                                                                 atTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGttt     >  1:2592434/1‑70 (MQ=255)
                                                                  ttGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGa                               >  1:5399976/1‑43 (MQ=255)
                                                                  ttGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGa                               >  1:3128781/1‑43 (MQ=255)
                                                                  ttGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGa   >  1:3276143/1‑71 (MQ=255)
                                                                  ttGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGa   >  1:4515181/1‑71 (MQ=255)
                                                                  ttGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGa   >  1:4137337/1‑71 (MQ=255)
                                                                    gCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGAc  >  1:4779950/1‑70 (MQ=255)
                                                                    gCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGAc  >  1:4731542/1‑70 (MQ=255)
                                                                     |                                                                    
CGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGAC  >  minE/1259781‑1259918

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