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 F44 I1 R1 12 24.7 574166 94.6% 543161 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,462,758 G→A A70T (GCA→ACA)  USA300HOU_RS12680 → Putative 3‑methyladenine DNA glycosylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,462,7580GA94.7% 43.6 / NA 19A70T (GCA→ACA) USA300HOU_RS12680Putative 3‑methyladenine DNA glycosylase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (11/7);  minor base C (1/0);  total (12/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATACCACTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGG  >  USA300TCH1516_ALE/2462620‑2462882
                                                                                                                                          |                                                                                                                            
gATACCACTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATAca                                                                                                                            >  1:202041/1‑141 (MQ=255)
       cTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCa                                                                                                                     >  1:15491/1‑141 (MQ=255)
        tCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCAt                                                                                                                    >  1:193433/1‑141 (MQ=255)
            aCGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATCCAt                                                                                                                >  2:218510/1‑141 (MQ=255)
               tataCAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATTGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACg                                                                                                             <  2:91863/141‑1 (MQ=255)
                 taCAGGCTACATCGTGGAAACGGAAGCTTACCTAGGTTTGACTGATCGGGCGGCTCATGGCTATGGCAGTCAAATAACAACTAACGTCACGTCATTATATAAACGTGGTGGTACAATTTCTCCACATGTCATGTATACGCa                                                                                                           >  2:47262/1‑141 (MQ=255)
                       cTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACt                                                                                                     >  1:118637/1‑141 (MQ=255)
                            tCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGAGATAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTGCTCATTa                                                                                                >  1:256152/1‑141 (MQ=255)
                                            ttacttaGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATc                                                                                <  2:180365/141‑1 (MQ=255)
                                             tacttaGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATGAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTAATCATTAATTTTGTAAGAAGATCt                                                                               >  1:92622/1‑141 (MQ=255)
                                                                     gCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACtt                                                       >  2:234783/1‑141 (MQ=255)
                                                                                 ggCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGATACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAAtt                                           <  1:101506/141‑1 (MQ=255)
                                                                                  gCGGTAAGATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACAGGTCATGCATACGCAGTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTg                                          <  2:4599/141‑1 (MQ=255)
                                                                                    ggTAAAATAACAGCTAGAGTCACGTCAGAATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGACGTACTTATCCGCACAATTGaa                                        >  2:160555/1‑141 (MQ=255)
                                                                                               acatataGTCAATTCATGATATAAACGTGGTGGTACAATTTATACACATGTGATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAgg                             <  2:99684/135‑1 (MQ=255)
                                                                                                  tAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGttt                          <  2:193433/141‑1 (MQ=255)
                                                                                                                tatataAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTcc            <  2:202041/141‑1 (MQ=255)
                                                                                                                    taAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCCCAATTGAACCAGAACAAGGTTTCCCCGCTATGTTCCGTaa        >  2:244003/1‑141 (MQ=255)
                                                                                                                          tggtggTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGGAGAAGGTTTATCCGCTATGTTCCGTGACAGAgg  >  1:70038/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                            
GATACCACTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGG  >  USA300TCH1516_ALE/2462620‑2462882

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