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 F1 I1 R1	502	34.8	1912488	98.2%	1878063	80.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,584,652	(T)_6→8	intergenic (+93/‑107)	yrhD → / → yrhB	uncharacterized protein YrhD/putative heat shock chaperone

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,584,646	1	.	T	100.0%	35.5 / NA	11	intergenic (+87/‑113)	yrhD/yrhB	uncharacterized protein YrhD/putative heat shock chaperone
Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (6/5); total (6/5)
*	NC_000913	3,584,646	2	.	T	100.0%	35.8 / NA	11	intergenic (+87/‑113)	yrhD/yrhB	uncharacterized protein YrhD/putative heat shock chaperone
Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (6/5); total (6/5)

AATCCCGTTCGACGTTCTGAAAAAGAAATCATAAAATATTAGCAGATACTTATTTCGTGACTATATCTTATCCGATGAAC‑‑‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTCTTTGCTCAATGTATCACAC  >  NC_000913/3584567‑3584715

||

aaTCCCGTTCGACGTTCTGAAAAAGAAATCATAAAATATTAGCAGATACTTATTTCGTGACTATATCTTATCCGATGAAC‑‑‑t                                                                      <  2:682444/81‑1 (MQ=255)

          gACGTTCTGAAAAAGAAATCATAAAATATTAGCAGATACTTATTTCGTGACTATATCTTATCCGATGAAC‑‑‑ttttttttca                                                             >  1:682461/1‑76 (MQ=255)

                   aaaaaGAAATCATAAAATATTAGCAGATACTTATTTCGTGACTATATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCAt                                                     >  1:682475/1‑81 (MQ=255)

                       aGAAATCATAAAATATTAGCAGATACTTATTTCGTGACTGTATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTtaa                                                 >  1:682472/1‑81 (MQ=255)

                                aaaaTATTAGCAGATACTTATTTCGTGACTATATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCtt                                        >  2:682459/1‑81 (MQ=255)

                                 aaaTATTAGCAGATACTTATTTCGTGACTATATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCttt                                       >  1:682477/1‑81 (MQ=255)

                                        aGCAGATACTTATTTCGTGACTATATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACg                                   >  2:682469/1‑78 (MQ=255)

                                                    tttCGTGACTATATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTc                     <  1:682445/80‑1 (MQ=255)

                                                    tttCGTGACTATATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTc                     <  2:682446/80‑1 (MQ=255)

                                                        gTGACTATATCTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTCTTTGc                <  1:682447/81‑1 (MQ=255)

                                                               tatCTTATCCGATGAACTTTTTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTCTTTGCTCAAt           <  2:682448/80‑1 (MQ=255)

                                                                  cTTATCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTCTTTGCTCAATGTAt       >  2:682466/1‑80 (MQ=255)

                                                                      tCCGATGAACTT‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTCTTTGCTCAATGTATcacac  <  1:682449/81‑1 (MQ=255)

||

AATCCCGTTCGACGTTCTGAAAAAGAAATCATAAAATATTAGCAGATACTTATTTCGTGACTATATCTTATCCGATGAAC‑‑‑TTTTTTCAAAACCAGCATTTAATAATATCTTTGACGAAGATGAACGCGTCTTTGCTCAATGTATCACAC  >  NC_000913/3584567‑3584715

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A