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 F28 I1 R2	164	48.3	4710601	85.3%	4018142	55.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,407,692	C→T	R325C (CGT→TGT)	hflK →	modulator for HflB protease specific for phage lambda cII repressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,407,692	0	C	T	100.0%	141.6 / NA	43	R325C (CGT→TGT)	hflK	modulator for HflB protease specific for phage lambda cII repressor
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (25/18); total (25/18)

CTTTGCTAAACTTCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGCGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCAAAGTGCTGGTTAA  >  W3110S.gb/4407640‑4407750

cTTTGCTAAACTTCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGtata                                                   <  1:2579684/62‑1 (MQ=255)

 tttGCTAAACTTCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTg                                                       >  1:2986612/1‑57 (MQ=255)

            tCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATgg                                       <  1:3250380/62‑1 (MQ=255)

            tCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATgg                                       <  1:600877/62‑1 (MQ=255)

            tCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATgg                                       <  1:1587953/62‑1 (MQ=255)

            tCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATgg                                       <  1:1809660/62‑1 (MQ=255)

            tCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATgg                                       <  1:4424126/62‑1 (MQ=255)

            tCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATgg                                       <  1:3702767/62‑1 (MQ=255)

                    aaTATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGATACGATGGa                                      >  1:4704726/1‑55 (MQ=255)

                    aaTATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGaa                                     >  1:3866413/1‑56 (MQ=255)

                    aaTATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGaa                                     >  1:4446376/1‑56 (MQ=255)

                    aaTATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGaa                                     >  1:3673913/1‑56 (MQ=255)

                    aaTATAAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGaa                                     >  1:1659441/1‑56 (MQ=255)

                        taAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTatat                                                  <  1:3662360/39‑1 (MQ=255)

                        taAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTatat                                                  <  1:3089429/39‑1 (MQ=255)

                        taAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTatat                                                  <  1:4090401/39‑1 (MQ=255)

                        taAAGCCGCGCCGGAAATTACTCGCGAGTGTCTGTatat                                                  <  1:334380/39‑1 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGATTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:4205373/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:3819709/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:39098/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:4298520/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:3511506/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:4530773/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:2508281/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:2006858/1‑62 (MQ=255)

                            gCCGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTaa                       >  1:1035962/1‑62 (MQ=255)

                             ccGCGCCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAac                      <  1:1993751/62‑1 (MQ=255)

                               gcgcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTgg                           >  1:37800/1‑55 (MQ=255)

                               gcgcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAacac                    >  1:4120166/1‑62 (MQ=255)

                               gcgcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAacac                    >  1:1065814/1‑62 (MQ=255)

                               gcgcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAacac                    >  1:3012398/1‑62 (MQ=255)

                               gcgcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAacac                    >  1:2842430/1‑62 (MQ=255)

                               gcgcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAaca                     >  1:3548375/1‑61 (MQ=255)

                               gcgcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAaca                     >  1:839615/1‑61 (MQ=255)

                                 gcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACAcc                   >  1:3836237/1‑61 (MQ=255)

                                 gcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACAcc                   >  1:2647578/1‑61 (MQ=255)

                                 gcCGGAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACAcc                   >  1:2119764/1‑61 (MQ=255)

                                    ggAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCa               <  1:2579922/62‑1 (MQ=255)

                                    ggAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCa               <  1:128940/62‑1 (MQ=255)

                                     gAAATTACTCGCGAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCa               <  1:3259795/61‑1 (MQ=255)

                                                 gAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCAAAGTGCTGGTTaa  <  1:3862039/62‑1 (MQ=255)

                                                 gAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCAAAGTGCTGGTTaa  <  1:3959939/62‑1 (MQ=255)

                                                 gAGTGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCAAAGTGCTGGTTaa  <  1:3270125/62‑1 (MQ=255)

CTTTGCTAAACTTCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGCGTCTGTATATCGAGACGATGGAAAAAGTGTTGGGTAACACCCGCAAAGTGCTGGTTAA  >  W3110S.gb/4407640‑4407750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A