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
A19 F74 I0 R1	21	36.7	824702	95.0%	783466	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,269	G→A	84.5%	P126S (CCA→TCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,269	0	G	A	84.5%	46.4 / 4.0	26	P126S (CCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (2/2); new base A (10/12); total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.04e-01

TGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAG  >  USA300TCH1516_ALE/2028136‑2028405

tGCACGTTGCCTAAAATGTGTCTAATAACAATGGTATGATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTTCGt                                                                                                                                   <  2:383863/141‑1 (MQ=255)

    cTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGGTGCt                                                                                                                               >  1:209686/1‑141 (MQ=255)

      ttACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCa                                                                                                                             <  2:42579/141‑1 (MQ=255)

      ttACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCa                                                                                                                             >  1:89013/1‑141 (MQ=255)

                   gtCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACtttt                                                                                                                >  1:140606/1‑141 (MQ=255)

                                 gTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTTTACGTTGCTCACCAAACCACTTTTGTTTAATACAAGAt                                                                                                  >  2:134550/1‑141 (MQ=255)

                                 gTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAACGAt                                                                                                  >  2:79841/1‑141 (MQ=255)

                                 gTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATACAAAAt                                                                                                  >  2:286523/1‑141 (MQ=255)

                                 gTATTATTTTCCTGAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGAAAGCAAGTCCAGGTTGAATTTGTACATCTTCCCACTTATATACGTTGACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGAt                                                                                                  <  2:167381/141‑1 (MQ=255)

                                           ccTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCa                                                                                        <  1:19619/141‑1 (MQ=255)

                                                atatTTGCAGGTTTTGTTGAGTCGATATGGACGTCGCACAGTGCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAAcc                                                                                   <  2:145426/141‑1 (MQ=255)

                                                     tGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATc                                                                              <  2:48745/141‑1 (MQ=255)

                                                                 tAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCTCGactcc                                                                  >  2:264079/1‑139 (MQ=255)

                                                                         tatGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAACCCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTg                                                          >  2:28983/1‑141 (MQ=255)

                                                                            gTAGTTCTCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGtt                                                       <  2:385218/141‑1 (MQ=255)

                                                                            gTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTAACAGGATTGGGGTTGTTTAATTCATAAGTGTCAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGtt                                                       <  1:302799/141‑1 (MQ=255)

                                                                                         tCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTAt                                          <  2:381359/141‑1 (MQ=255)

                                                                                            aTGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTaa                                       <  2:16801/141‑1 (MQ=255)

                                                                                                  aaTTTGTACATCTTCCCACTTATATACATAAACTGATGTACGGTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACg                                 <  2:309107/141‑1 (MQ=255)

                                                                                                     ttGTACATCTTCCCACTAATATACATAAACTGATGTACGTTGCTCATCAAACCACTTTTGTTTAATAAAAAATGGTGAAGTCATAACCTCATACATCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGcac                              <  2:197472/141‑1 (MQ=255)

                                                                                                           aTCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAg                        >  1:30402/1‑141 (MQ=255)

                                                                                                            tCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCACCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGt                       <  1:209668/141‑1 (MQ=255)

                                                                                                                cccACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCCTCCGTCGCAACTACTTTTTTTGGTTTAATCTTCTGGATGAAAGATCGCACAGTAAGtacta                   >  1:173751/1‑141 (MQ=255)

                                                                                                                    cTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCACCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTAATAAATAACTCACAATAAGtcataataa               >  2:119735/1‑141 (MQ=255)

                                                                                                                     ttATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGAAATAATaaa              >  1:332406/1‑141 (MQ=255)

                                                                                                                                 aCTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAg  <  2:140606/141‑1 (MQ=255)

TGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAG  >  USA300TCH1516_ALE/2028136‑2028405

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