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
A9 F59 I1 R1	29	14.4	307489	99.5%	305951	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,642,589	G→A	intergenic (‑19/+120)	USA300HOU_RS13595 ← / ← yccS	hypothetical protein/Inner membrane protein YccS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,642,589	0	G	A	100.0%	41.5 / NA	13	intergenic (‑19/+120)	USA300HOU_RS13595/yccS	hypothetical protein/Inner membrane protein YccS
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (7/6); total (7/6)

GAACAACATCTTTTTCAAGATATCCTTCTTTTAACATTGCATTCGCAATTTCTATCGCTTTTTGCCGTTTAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTC  >  USA300TCH1516_ALE/2642447‑2642729

gAACAACATCTTTTTCAAGATATCCTTCTTTTAACATTGCATTCGCAATTTCTATCGCTTTTTGCCGTTTAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATtata                                                                                                                                         <  1:34257/148‑1 (MQ=255)

        tCTTTTTCAAGATATCCTTCTTTTAACATTGCATTCGCAATTTCTATCGCTTTTTGCCGTTTAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTCATGt                                                                                                                                 >  1:112612/1‑148 (MQ=255)

        tCTTTTTCAAGATATCCTTCTTTTAACATTGCATTCGCAATTTCTATCGCTTTTTGCCGTTTAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTCATGt                                                                                                                                 >  1:242410/1‑148 (MQ=255)

                               tAACATTGCATTCGCAATTTCTATCGCTTTTTGCCGTTTAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTGATGTTATATACCACCATAATTATaaaa                                                                                                          >  1:294582/1‑148 (MQ=255)

                                                          tttttGCCGTTTAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCTCTTCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTCAACACATTTTTTTaa                                                                               >  1:42443/1‑147 (MQ=255)

                                                                     tAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCat                                                                    <  1:211735/148‑1 (MQ=255)

                                                                          aCTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCAtaataa                                                               >  1:58965/1‑148 (MQ=255)

                                                                                          aTTTTTCTGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTATACTCCCGTCATAATAACTTCAGACAAACGTTa                                               <  1:95329/148‑1 (MQ=255)

                                                                                                  gggTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGAcc                                       <  1:279849/148‑1 (MQ=255)

                                                                                                    gTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTg                                     <  1:189812/148‑1 (MQ=255)

                                                                                                                          aTTTCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGt               <  1:76572/148‑1 (MQ=255)

                                                                                                                           tttCCTTAACCTCCAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGtt              >  1:158959/1‑148 (MQ=255)

                                                                                                                                       ccAATATATTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTACCGTCCTAATAAATTCAGACACTCGTTAGTATGACCTGATAAATATTTAATTTTACACGTTCTTGtctctctc  >  1:275445/1‑148 (MQ=255)

GAACAACATCTTTTTCAAGATATCCTTCTTTTAACATTGCATTCGCAATTTCTATCGCTTTTTGCCGTTTAATTACTTCAAATTCTTTCCATTTTTCGGGGTAACCTTTCATTGTAAAGGGCATTTCCTTAACCTCCAATATGTTATAATTCATGTTATATACCACCATAATTATAAAATGAAACATATTAAACACATTTTTTTAGACTCCCGTCATAATAACTTCAGACAAACGTTAGTCTGACCTGATAAATATTTAATTTTAAACGTTCTTGTCTCTCTC  >  USA300TCH1516_ALE/2642447‑2642729

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

GATK/CNVnator alignment

N/A