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
A5 F71 I1 R1	31	24.1	564604	94.3%	532421	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,220,870	(A)_6→7	intergenic (‑521/+41)	USA300HOU_RS11345 ← / ← atpC	hypothetical protein/ATP synthase epsilon chain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,220,864	1	.	A	91.3%	64.8 / ‑0.8	23	intergenic (‑515/+47)	USA300HOU_RS11345/atpC	hypothetical protein/ATP synthase epsilon chain
Reads supporting (aligned to +/- strand): ref base . (2/0); new base A (7/14); total (9/14)
Fisher's exact test for biased strand distribution p-value = 1.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑A‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTATTGTCGTCATCATTTT  >  USA300TCH1516_ALE/2220724‑2220999

attattACTAATATATTCATATTTTTAAATACAGATTAGCTGTTATTAATGATAAAAAACCACTACATCATAAATCTTTAATGTTTCTTTATAAATTCCTACCAACCTCTCATATTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           <  2:252782/137‑1 (MQ=255)

aGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATATAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           >  1:122942/1‑141 (MQ=255)

aGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           >  1:136773/1‑141 (MQ=255)

aGTTTTACTCATGTATTCCTAATTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTc                                                                                                                                           <  2:182260/141‑1 (MQ=255)

    ttACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCACCCATCTCATGTTTTGTATTTTTAAATAAATATATTTT‑a‑aaa                                                                                                                                     >  2:141859/1‑141 (MQ=25)

     tACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTT‑a‑aaaa                                                                                                                                    >  1:248409/1‑141 (MQ=255)

      aCTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑a‑aaaaa                                                                                                                                   <  1:95153/141‑1 (MQ=255)

      aCTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCCTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑a‑aaaaa                                                                                                                                   <  1:203438/141‑1 (MQ=255)

       cTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑a‑caaaaa                                                                                                                                  >  1:48499/1‑140 (MQ=255)

              aTTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCATCCACCCTCTCAGGTTTTGTCCCTTTAAATCAATATAATTC‑A‑AAAAAaggggcga                                                                                                                           >  1:38870/1‑136 (MQ=37)

                tCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAg                                                                                                                          <  1:258132/141‑1 (MQ=255)

                 ccTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCGTTATAAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGa                                                                                                                         <  2:131939/141‑1 (MQ=255)

                    tttttcAAATACACCTTAACAGTACATAATCATAAAGAGCCACTACATCATAAATCTTTAATGGTTCTTAATCAATTCCTCACCCCCCCTCATGCTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:234608/140‑1 (MQ=255)

                    ttttgtAAATAGACATTATCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCGTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:270167/140‑1 (MQ=38)

                    atgtttAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:132558/138‑1 (MQ=255)

                    aTTTTTAAATACACATTAGCTTTGTTTAATGATAAAGAAACACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGatat                                                                                                                      <  2:239549/141‑1 (MQ=255)

                           aaTACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATca                                                                                                               <  1:13630/141‑1 (MQ=255)

                                                     aaaGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTAttt                                                                                     <  2:83965/141‑1 (MQ=255)

                                                                 catcatAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGCCGAAGATATGAACTCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCcac                                                                         >  1:8327/1‑141 (MQ=255)

                                                                     atAGATCTTGTATGGTTGGTTATCAAGTCGTTACCCCCTCTAATGTTTTGTATCTTTAAATCAATATGATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCGACACGc                                                                     <  2:133446/141‑1 (MQ=255)

                                                                        aaTCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCaaa                                                                  >  1:242982/1‑141 (MQ=255)

                                                                            tttAATGGTTCTTTATCAATTCCTTCCCCCCTATCATGTTTTGTATCTTTAAATCAATATAATTC‑ACACAAAGTTTCGAAGATATTAAACCACATCTTCGACCCTCTCTTTACTATTTTAATTCAGCCCCACTCacactct                                                              >  2:248869/1‑138 (MQ=255)

                                                                               aaTGGTTCTTTATCAATTCCTTCCCCCCTGTCATGTTTTGTATCTTTACATCAATATAATTCAA‑AAAAAGGGTCGAAGATATAAAATCACAACTTCGACCCTTTATTTACTATTTTAATTCACCCCCCCGCCACCGGTAAt                                                           >  2:280974/1‑141 (MQ=255)

                                                                                            cAATTCCTGCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTaa                                              <  1:274571/141‑1 (MQ=255)

                                                                                               ttccttccCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGc                                           <  2:122942/141‑1 (MQ=255)

                                                                                               ttccttccCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGc                                           <  2:136773/141‑1 (MQ=255)

                                                                                                   ttccACCATCTAAAGTTTTGTCCCTTTACATAATGATAATTCAA‑AAAAAGGGTCGAAGAAATAAGATTGCATCTTCGACGCTTGGTAGACTATTTTAATTCAGCCACACGCAAACGGTTATGTGCTCTCTCTAAGGGTCtt                                       >  2:5106/1‑141 (MQ=255)

                                                                                                            ctcATGTTTTGTATCTTTAAATCAATATAATTCAA‑AAAAAGGGACGCACATTTGTAATACCATGGACGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTa                              >  1:280561/1‑141 (MQ=255)

                                                                                                                          ttttAAATCAATATAATTCAA‑AAAAAGGGTCGAAGATATGAAATCACTTTGTCTACTCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTAtt                <  2:242982/140‑1 (MQ=255)

                                                                                                                                    atatAATTCAA‑AAAAAGGGACGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGTCTCTATGAATATTAGTATTGTCGtcatct      >  1:272486/1‑140 (MQ=255)

                                                                                                                                       taATTCAA‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGAACCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTATTGTCGTCATCAttt   <  1:192829/141‑1 (MQ=255)

                                                                                                                                        aaTTCAA‑AAAAAGGATCGAAGATAAGAAATCACATCTTCGACCCTTTATTTACTATTTTAACTCAGCCACACGCCAACGGTTACTCGCTCTCTCTAAAGCCCTTTCGCCCCTATCAATATCAGCATCACCGCCATCAtttc  >  2:22453/1‑140 (MQ=255)

AGTTTTACTCATGTATTCCTATTTTTAAATACACATTAGCTGTGTTTAATGATAAAGAACCACTACATCATAAATCTTTAATGGTTCTTTATCAATTCCTTCCCCCCTCTCATGTTTTGTATCTTTAAATCAATATAATTC‑A‑AAAAAGGGTCGAAGATATGAAATCACATCTTCGACCCTTTATTTACTATTTTAATTCAGCCACACGCAAACGGTTATTTGCTCTCTCTAAAGCTCTTTCGGCTCTATGAATATCAGTATTGTCGTCATCATTTT  >  USA300TCH1516_ALE/2220724‑2220999

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A