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
A23 F59 I1 R1 23 28.6 559496 98.6% 551663 149.0

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% 95.4 / NA 29intergenic (+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 (11/18);  total (11/18)

ACAATCAAACAGATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACT  >  USA300TCH1516_ALE/2343292‑2343563
                                                                                                                                                  |                                                                                                                             
aCAATCAAACAGATACAAAGTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATaa                                                                                                                             >  2:177518/1‑149 (MQ=255)
      aaaCAGATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTaa                                                                                                                       <  2:272297/149‑1 (MQ=255)
              aCAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTtata                                                                                                               >  1:187745/1‑149 (MQ=255)
              aCAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTtata                                                                                                               >  1:187781/1‑149 (MQ=255)
              aCAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTtata                                                                                                               >  2:191516/1‑149 (MQ=255)
               cAAATTGTAGGTAAATAATAATTTGAAAATAGTTGTATAGGGCAAGCGCTGGAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTatat                                                                                                              <  1:22775/149‑1 (MQ=255)
                   ttGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAgt                                                                                                          >  1:213486/1‑149 (MQ=255)
                            aataataatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACcac                                                                                                 <  1:55018/149‑1 (MQ=255)
                               aataatTTGAAAAGAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTATTTAGTTATTGCAGTTGTAAATTATTTTTGTGTGCGTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAAt                                                                                              <  1:26390/149‑1 (MQ=255)
                                      tGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAAt                                                                                       <  2:191498/149‑1 (MQ=255)
                                          aaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTaa                                                                                   <  2:3453/149‑1 (MQ=255)
                                                       ggCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTTTTGAACTTGTAAATTATTGTTGTTTGCTTCGCGTAGGATCATATTGGCCTATATATTAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCaaa                                                                      >  1:265082/1‑149 (MQ=255)
                                                       ggCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCaaa                                                                      >  1:167612/1‑149 (MQ=255)
                                                             cgcTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCaa                                                                >  2:59996/1‑149 (MQ=255)
                                                                       ttGGCGCTGGTCCTTTTAGATATTGAACTTGTAGAGTATTGTTGTGTGCTTCTCGTAGTAACAGATACGCCTATATAATAGTAAAAATTATATGGGTGTGTACCACAATTTATAGTCTAAACATAACAGCAAAGCTCAAATATCTGGaa                                                      <  2:227381/149‑1 (MQ=255)
                                                                         ggCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAAcc                                                    <  2:187745/149‑1 (MQ=255)
                                                                         ggCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAAcc                                                    <  2:187781/149‑1 (MQ=255)
                                                                         ggCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAAcc                                                    <  1:191516/149‑1 (MQ=255)
                                                                                 tCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAAt                                            <  1:243796/149‑1 (MQ=255)
                                                                                              tGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACCTAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTg                               <  2:222702/149‑1 (MQ=255)
                                                                                              tGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTg                               <  1:214377/149‑1 (MQ=255)
                                                                                              tGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTg                               <  2:40670/149‑1 (MQ=255)
                                                                                                 aCTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTa                            <  2:147189/149‑1 (MQ=255)
                                                                                                           tattGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAgg                  >  2:43414/1‑149 (MQ=255)
                                                                                                             ttgttgTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGa                <  2:84496/149‑1 (MQ=255)
                                                                                                                 tgttTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGattta            >  1:28645/1‑149 (MQ=255)
                                                                                                                      gCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGAtttatttta       >  1:102793/1‑149 (MQ=255)
                                                                                                                        ttCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATttattttatt     <  2:65016/149‑1 (MQ=255)
                                                                                                                           tcatagtaACAGATTTGCCTATATAATAGTAACTTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCCAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACt  <  2:38110/146‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                             
ACAATCAAACAGATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACT  >  USA300TCH1516_ALE/2343292‑2343563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A