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
A19 F106 I1 R1 27 57.4 1363720 95.8% 1306443 135.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,343,438 C→T intergenic (+114/+250) USA300HOU_RS11955 → / ← aldC_1 65 kDa membrane protein/Alpha‑acetolactate decarboxylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,343,4380CT100.0% 108.0 / NA 36intergenic (+114/+250)USA300HOU_RS11955/aldC_165 kDa membrane protein/Alpha‑acetolactate decarboxylase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/16);  total (20/16)

AATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGAC  >  USA300TCH1516_ALE/2343309‑2343568
                                                                                                                                 |                                                                                                                                  
aaTTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAg                                                                                                                               <  1:113896/135‑1 (MQ=255)
     tAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAAt                                                                                                                          >  2:58189/1‑135 (MQ=255)
           aatcataatTTGAAAATAGTTTTATAGGGGAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTtata                                                                                                                    <  2:159769/135‑1 (MQ=255)
                      gAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTAc                                                                                                         >  2:400620/1‑135 (MQ=255)
                                 tataGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTtata                                                                                              >  2:542090/1‑135 (MQ=255)
                                    aGGGCAAGCGCTGAAAAATTGGCGATTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATc                                                                                           >  1:539731/1‑135 (MQ=255)
                                          aGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACa                                                                                     <  2:352461/135‑1 (MQ=255)
                                           gcgcTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATAGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACAt                                                                                    >  2:363874/1‑135 (MQ=255)
                                                 aaaaaTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGc                                                                              >  2:452111/1‑135 (MQ=255)
                                                     aTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATCTTAGTGAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAAt                                                                          >  1:452534/1‑135 (MQ=255)
                                                     aTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAAt                                                                          >  2:471450/1‑135 (MQ=255)
                                                     aTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAAt                                                                          >  2:283403/1‑135 (MQ=255)
                                                          tgTTGGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCaa                                                                     <  1:280495/134‑1 (MQ=255)
                                                           gTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATTTAAACATAACAGCAAATCTCaaa                                                                    <  1:371713/135‑1 (MQ=255)
                                                                        gTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATCATCTAAAAATAACAGCAAATCTCAAATTTCTTGAACCta                                                       <  2:30925/135‑1 (MQ=255)
                                                                        gTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCta                                                       <  2:153033/135‑1 (MQ=255)
                                                                        gTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCta                                                       <  2:652399/135‑1 (MQ=255)
                                                                         ttATTGAACTTGTAAATTCTTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATCTAATAGTAAAATTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTGAAACATCTGaaaacgaa                                                      >  2:427587/1‑130 (MQ=255)
                                                                              gAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAAt                                                 >  2:555110/1‑135 (MQ=255)
                                                                              gAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAAt                                                 >  1:362377/1‑135 (MQ=255)
                                                                              gAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAAt                                                 >  1:597737/1‑135 (MQ=255)
                                                                                aCTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATcc                                               >  1:160553/1‑135 (MQ=255)
                                                                                 cTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAAGccc                                              <  1:58189/135‑1 (MQ=255)
                                                                                 cTTGTAAATTATTGTTGGTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATccc                                              <  2:613213/135‑1 (MQ=255)
                                                                                  ttGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATcccc                                             >  2:404136/1‑135 (MQ=255)
                                                                                       aaTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTAAAATATCTGGAACCTAATAAATCCCCTCact                                        >  2:369859/1‑135 (MQ=255)
                                                                                             tgttgtTTGCTTCTCGTAGTAACAGAGTGGCCTATATAATAGTAAATTTTATAGGAGGGTGTACCACCATTTATAATCTAAACATAACAGCAAATCGCAAATATCTGGACCCTAATAAATCCCCTCACCactact                                  >  2:91473/1‑135 (MQ=255)
                                                                                                   ttGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAGTTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGt                            <  1:400620/135‑1 (MQ=255)
                                                                                                     gCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATTACAGCAAATCTTAAATATCTGGAATCTAATAAATTCCCTCACTACTGCTAATAGTGa                          <  1:63697/135‑1 (MQ=255)
                                                                                                          tcGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCTCTTCTGCTAATAGTGAAGGGa                     <  1:542090/135‑1 (MQ=255)
                                                                                                              agtaACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGattta                 <  1:446425/135‑1 (MQ=255)
                                                                                                               gtaACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCCCACTACTGCTAATAGTGAAGGGatttat                <  2:15238/135‑1 (MQ=255)
                                                                                                                    aGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACAACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATATGGAAGGGAtttattttat           >  2:382668/1‑135 (MQ=255)
                                                                                                                      aTTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTAATGCTACTAGAGAAGGGCgttattttatca         >  2:619331/1‑133 (MQ=255)
                                                                                                                         ggCCTATATAATAGTAAATTTTATATGAGTGTGTACAAAAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTCCTAATAGTGAAGGGAATTATTTTATTACtt      >  1:211979/1‑135 (MQ=255)
                                                                                                                          gCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTTGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACCTa     <  1:363874/135‑1 (MQ=255)
                                                                                                                             tatataATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAATTCCCCTCACTATTGCTAATAATGAAGGGATTTATTTTATTACCTAGAc  <  1:665595/135‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                  
AATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGAC  >  USA300TCH1516_ALE/2343309‑2343568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A