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 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,784,184 T→C 22.6% I223T (ATA→ACA)  yfjB → NAD kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,784,1840TC22.6% 120.2 / 35.6 62I223T (ATA→ACA) yfjBNAD kinase
Reads supporting (aligned to +/- strand):  ref base T (33/15);  new base C (5/9);  total (38/24)
Fisher's exact test for biased strand distribution p-value = 3.31e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

CCTCTCTGGATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAGTTGC  >  minE/1784118‑1784248
                                                                  |                                                                
ccTCTCTGGATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATaaa                                                               >  1:922224/1‑70 (MQ=255)
ccTCTCTGGATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCAATGGTCATaaa                                                               >  1:1915062/1‑70 (MQ=255)
      ttgATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagcag                                                         >  1:565088/3‑70 (MQ=255)
      tGGATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagcag                                                         >  1:163973/1‑70 (MQ=255)
      tGGATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagcag                                                         >  1:338714/1‑70 (MQ=255)
      tGGATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagcag                                                         >  1:363670/1‑70 (MQ=255)
        gATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagcagcag                                                      <  1:1552232/71‑1 (MQ=255)
        gATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagcag                                                         <  1:985786/68‑1 (MQ=255)
          tGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAgcagcagca                                                    >  1:1442741/1‑71 (MQ=255)
            cGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACg                                                  <  1:258148/71‑1 (MQ=255)
            cGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCACAAAcagcagc                                                        >  1:888917/1‑65 (MQ=255)
               ttACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATaaa                                                               >  1:797410/1‑55 (MQ=255)
               ttACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATc                                               <  1:1835545/71‑1 (MQ=255)
                tACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATcc                                              >  1:1868173/1‑71 (MQ=255)
                 aCCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATcc                                              <  1:1579244/70‑1 (MQ=255)
                 aCCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATcc                                              <  1:2070934/70‑1 (MQ=255)
                   ccTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTc                                           >  1:2081311/1‑71 (MQ=255)
                   ccTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTc                                           >  1:1083860/1‑71 (MQ=255)
                     tGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCt                                          >  1:127604/1‑70 (MQ=255)
                           ccATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGtttt                                   <  1:230425/71‑1 (MQ=255)
                             aTGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTc                                 >  1:1055379/1‑71 (MQ=255)
                               gTTCCCGCATACGTTGTCAGCACGACCACTGGTCATaaa                                                               >  1:1847602/1‑39 (MQ=255)
                               gTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCAc                                                   >  1:1852737/1‑51 (MQ=255)
                                ttCCCGCATACGTTGTCAGCACGACCCCTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCa                              >  1:1425980/1‑71 (MQ=255)
                                ttCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagc                                                           >  1:431829/1‑42 (MQ=255)
                                ttCCCGCATACGTTGTCAGCACGACCACTGGTCATAAAcagc                                                           >  1:1637501/1‑42 (MQ=255)
                                ttCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCa                              >  1:1692921/1‑71 (MQ=255)
                                ttCCCGCATACGTTGTCAGCACGACCACTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGc                               <  1:794664/70‑1 (MQ=255)
                                  cccGCATACGTTGTCAGCACGACCACTGGTCATAAAcag                                                            >  1:925839/1‑39 (MQ=255)
                                  cccGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATc                            >  1:1590319/1‑71 (MQ=255)
                                     gCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGcc                         <  1:280848/71‑1 (MQ=255)
                                     gCATACGTTGTCAGCACGACCACTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGcc                         >  1:984333/1‑71 (MQ=255)
                                      cATACGTTGTCAGCACGACCACTGGTCACAAACAGCAGCAGCACGATCCGTCTGAGTTTTTCGCATCGCCg                        >  1:1599156/1‑71 (MQ=255)
                                       aTACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGt                       <  1:1738664/71‑1 (MQ=255)
                                        tACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCa                              <  1:2068225/63‑1 (MQ=255)
                                          cGTTGTCAGCACGTCCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAAc                    >  1:2031970/1‑71 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTc                                           >  1:2046364/1‑48 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTaa                     >  1:1607741/1‑70 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTaa                     >  1:1545538/1‑70 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTaa                     >  1:1985487/1‑70 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAAc                    >  1:2198928/1‑71 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAAc                    >  1:25429/1‑71 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGcc                         >  1:25442/1‑66 (MQ=255)
                                          cGTTGTCAGCACGACCACTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAAc                    >  1:1942113/1‑71 (MQ=255)
                                             tGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGAc                 >  1:1109504/1‑71 (MQ=255)
                                             tGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGAc                 >  1:1034070/1‑71 (MQ=255)
                                                 aGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGt                       <  1:1720844/61‑1 (MQ=255)
                                                     cGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAAt         <  1:2178936/71‑1 (MQ=255)
                                                     cGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAAt         <  1:619383/71‑1 (MQ=255)
                                                      gACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTaa                     >  1:43092/1‑58 (MQ=255)
                                                      gACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATc        <  1:404612/71‑1 (MQ=255)
                                                         cACTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCg                                <  1:910485/44‑1 (MQ=255)
                                                         cACTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCg                                <  1:1907054/44‑1 (MQ=255)
                                                          aCTGGTCACAAACAGCAGCAGCACGATCTGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAGtt    <  1:509571/71‑1 (MQ=255)
                                                          aCTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAGtt    <  1:549439/71‑1 (MQ=255)
                                                          aCTGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAGtt    <  1:889790/71‑1 (MQ=255)
                                                            tGGTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGc                               <  1:1666523/42‑1 (MQ=255)
                                                              gTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAg      >  1:526096/1‑65 (MQ=255)
                                                              gTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAg      >  1:1446903/1‑65 (MQ=255)
                                                              gTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAGTTGc  <  1:1739824/69‑1 (MQ=255)
                                                              gTCACAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAGTTGc  <  1:1281133/69‑1 (MQ=255)
                                                                 aTAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCg                                <  1:264713/36‑1 (MQ=255)
                                                                  tAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGt                       <  1:1203957/44‑1 (MQ=255)
                                                                  |                                                                
CCTCTCTGGATGCGATTACCCTGGTGCCCATGTTCCCGCATACGTTGTCAGCACGACCACTGGTCATAAACAGCAGCAGCACGATCCGTCTGCGTTTTTCGCATCGCCGTAACGACCTGGAAATCAGTTGC  >  minE/1784118‑1784248

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