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 F75 I0 R1	16	35.0	795252	94.4%	750717	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,462,758	G→A	48.4%	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_ALE	2,462,758	0	G	A	48.4%	‑1.6 / 39.2	33	A70T (GCA→ACA)	USA300HOU_RS12680	Putative 3‑methyladenine DNA glycosylase
Reads supporting (aligned to +/- strand): ref base G (11/6); new base A (9/7); total (20/13)
Fisher's exact test for biased strand distribution p-value = 7.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.18e-01

CCACTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTAAGA  >  USA300TCH1516_ALE/2462624‑2462887

ccACTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTGATACACATg                                                                                                                             >  1:210348/1‑141 (MQ=255)

 cACTCAAACGTATACAGGCTACATAGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGTCGGTAAAATAACACCTAAAGTCAAGTCATTATATAAACGTACTAGTACAATTTATGCACAttt                                                                                                                            >  2:53786/1‑139 (MQ=255)

    tCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGGCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTAAt                                                                                                                         >  1:4976/1‑141 (MQ=255)

          gTATACAGGCTACATCGTGGAAACGGTAGTTTTCTTAGGTTTGAATGAGCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAGCGTGGTGGTACAATTTATACACATGTCATGCATAc                                                                                                                   <  2:27255/141‑1 (MQ=255)

          gTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATAc                                                                                                                   >  1:95940/1‑141 (MQ=255)

                    tACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTc                                                                                                         <  2:113100/141‑1 (MQ=255)

                     aCATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCa                                                                                                        >  1:4666/1‑141 (MQ=255)

                      aactgaggAAATGTAAGCTTACTTAGTTTTGAATGATCGTGCGACTCATTGCTATGGTGGTAAAATAACACCTAAAGTCACGTTATTATATAAACGTTTTGGTACAATTTATACACATGTCATGCATACGCATTTACTCAt                                                                                                       <  2:208007/135‑1 (MQ=255)

                            ggAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAAttt                                                                                                 >  1:216522/1‑141 (MQ=255)

                              aaaCGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTg                                                                                               <  1:122465/141‑1 (MQ=255)

                              aaaCGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACATAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTg                                                                                               >  2:161460/1‑141 (MQ=255)

                               aaCGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGt                                                                                              >  1:245703/1‑141 (MQ=255)

                                       cttacttaGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAAt                                                                                      <  1:304759/141‑1 (MQ=255)

                                                      aTGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTg                                                                       <  1:340491/141‑1 (MQ=255)

                                                          tCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCAAATGAACAATATACGCATCTGCACATTATTTTTGTAACAAAATATAAAGGTATACCTGAAgg                                                                   >  2:364658/1‑141 (MQ=255)

                                                              gCGGCTCATGGCTATGGCGGTAACATAACCCCTAAATCCACGGCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTa                                                               >  1:171553/1‑141 (MQ=255)

                                                                 gCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCCGAAGGCGTACtt                                                            >  1:119853/1‑141 (MQ=255)

                                                                   tCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAACCTGTAGCTCTAACTGAAGACGTACttct                                                          >  2:337213/1‑139 (MQ=255)

                                                                               gagTAAAATAACAACTAAAGTCACGTCATTATATAAACGTGGTGTTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGa                                              <  2:110625/139‑1 (MQ=255)

                                                                                    aaaTAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCag                                         <  1:392925/141‑1 (MQ=255)

                                                                                      aTAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCagaa                                       <  2:55616/141‑1 (MQ=255)

                                                                                           acCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATATACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAgg                                  <  1:264676/141‑1 (MQ=255)

                                                                                                acgTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTAt                             >  2:390393/3‑141 (MQ=255)

                                                                                                aaGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTAt                             >  1:367345/1‑141 (MQ=255)

                                                                                                   tCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCg                          <  2:171553/141‑1 (MQ=255)

                                                                                                     aCGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCAGAGCAATTGAACCAGAAGAAGGTTTATCCgtt                        >  2:231013/1‑139 (MQ=255)

                                                                                                     aCGTCATTATATAAACGTGGTGGGACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCt                        <  2:253214/141‑1 (MQ=255)

                                                                                                           tgatagaAACGTGGTGGTGAAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTc                  <  2:95940/139‑1 (MQ=255)

                                                                                                               ataAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTGGTAACAAAATGTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGATTTATCCGCGATATTCCGTa              >  1:251821/1‑141 (MQ=255)

                                                                                                                     gtggtgGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGAGTATCCGCTATGTTCCGTGACagag        >  1:363216/1‑141 (MQ=255)

                                                                                                                        gtggtACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCCATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTCACAGAGGTa     >  2:372262/1‑141 (MQ=255)

                                                                                                                         tggtACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTaa    >  2:12162/1‑141 (MQ=255)

                                                                                                                           gtACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATAGCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTaaaa  >  2:222668/1‑139 (MQ=255)

CCACTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTAAGA  >  USA300TCH1516_ALE/2462624‑2462887

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