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 I0 R1	64	42.0	921266	98.7%	909289	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,462,758	G→A	25.0%	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	25.0%	85.5 / 25.5	44	A70T (GCA→ACA)	USA300HOU_RS12680	Putative 3‑methyladenine DNA glycosylase
Reads supporting (aligned to +/- strand): ref base G (11/22); new base A (5/6); total (16/28)
Fisher's exact test for biased strand distribution p-value = 4.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

CTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTAAGAAAGGCTACGA  >  USA300TCH1516_ALE/2462627‑2462897

cTCAAACGTATACAGGCTAAATCATGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCa                                                                                                                                    <  2:175147/141‑1 (MQ=255)

       gTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATAc                                                                                                                             >  2:169248/1‑141 (MQ=255)

       gTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATAc                                                                                                                             >  2:219250/1‑141 (MQ=255)

            cAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTTAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAtt                                                                                                                        <  2:357182/141‑1 (MQ=255)

            cAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAtt                                                                                                                        <  2:448806/141‑1 (MQ=255)

            cAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAtt                                                                                                                        <  2:260501/141‑1 (MQ=255)

            cAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAtt                                                                                                                        <  2:275732/141‑1 (MQ=255)

            cAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAtt                                                                                                                        <  1:300236/141‑1 (MQ=255)

             aGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTACAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAttt                                                                                                                       <  1:365183/141‑1 (MQ=255)

             aGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAttt                                                                                                                       <  1:145397/141‑1 (MQ=255)

             aGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAttt                                                                                                                       <  1:258360/141‑1 (MQ=255)

             aGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCAttt                                                                                                                       <  1:269526/141‑1 (MQ=255)

                    aTCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCAtt                                                                                                                >  2:255383/1‑141 (MQ=255)

                      cGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTaa                                                                                                              >  2:379558/1‑141 (MQ=255)

                      cGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTaa                                                                                                              >  1:330778/1‑141 (MQ=255)

                      cGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTaa                                                                                                              >  2:295759/1‑141 (MQ=255)

                         ggAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAAttt                                                                                                           <  1:323902/141‑1 (MQ=255)

                         ggAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAAttt                                                                                                           <  1:400612/141‑1 (MQ=255)

                            aaCGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGt                                                                                                        >  1:182835/1‑141 (MQ=255)

                                        cttaGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGa                                                                                            <  1:219250/141‑1 (MQ=255)

                                                  aaTGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCt                                                                                  >  1:348368/1‑141 (MQ=255)

                                                  aaTGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCt                                                                                  >  2:243018/1‑141 (MQ=255)

                                                       tCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAgg                                                                             >  2:44228/1‑141 (MQ=255)

                                                       tCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAgg                                                                             >  2:97525/1‑141 (MQ=255)

                                                                    ggCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCcgc                                                                <  1:255383/141‑1 (MQ=255)

                                                                      cTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCgcgc                                                              >  1:348934/1‑141 (MQ=255)

                                                                                     aaCACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCagaaga                                               <  1:155357/141‑1 (MQ=255)

                                                                                     aaCACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCagaaga                                               <  2:128678/141‑1 (MQ=255)

                                                                                     aaCACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCagaaga                                               <  1:284384/141‑1 (MQ=255)

                                                                                      acacCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAgaagaa                                              <  2:348368/141‑1 (MQ=255)

                                                                                      acacCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAgaagaa                                              <  1:243018/141‑1 (MQ=255)

                                                                                                tCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCg                                    <  1:327112/141‑1 (MQ=255)

                                                                                                tCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCg                                    <  2:392438/141‑1 (MQ=255)

                                                                                                   cGTCATTATATAAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTCATCCGCGCAATTGAACCAGAAGAAGGTTTATCAGCTa                                 >  1:246696/1‑141 (MQ=255)

                                                                                                           tataAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGt                         <  2:182835/141‑1 (MQ=255)

                                                                                                             taAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGCACCAGAAGAAGGTTTATCCGCTATGTTCCGTaa                       <  2:366687/141‑1 (MQ=255)

                                                                                                             taAACGTGGTGGTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAAACTGAAGGTATACCTGAAGGCGTACTTACCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTCCCGTaa                       <  2:402189/141‑1 (MQ=255)

                                                                                                              aaaCGTGGTGGTACAATTTATACACATGTCATGCATGCGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCGGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAAc                      <  2:249414/141‑1 (MQ=255)

                                                                                                                   tggtggTACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAgg                 <  2:104262/141‑1 (MQ=255)

                                                                                                                      tggtACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTaa              >  1:189194/1‑141 (MQ=255)

                                                                                                                      tggtACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTaa              >  1:42237/1‑141 (MQ=255)

                                                                                                                      tggtACAATTTATACACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTaa              >  1:187165/1‑141 (MQ=255)

                                                                                                                                  tGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTAAGAAAGGCTACGa  <  1:97525/141‑1 (MQ=255)

                                                                                                                                  tGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTAAGAAAGGCTACGa  <  1:44228/141‑1 (MQ=255)

CTCAAACGTATACAGGCTACATCGTGGAAACGGAAGCTTACTTAGGTTTGAATGATCGTGCGGCTCATGGCTATGGCGGTAAAATAACACCTAAAGTCACGTCATTATATAAACGTGGTGGTACAATTTATGCACATGTCATGCATACGCATTTACTCATTAATTTTGTAACAAAATCTGAAGGTATACCTGAAGGCGTACTTATCCGCGCAATTGAACCAGAAGAAGGTTTATCCGCTATGTTCCGTAACAGAGGTAAGAAAGGCTACGA  >  USA300TCH1516_ALE/2462627‑2462897

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `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