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
A2 F1 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,698,231	T→C	Y107C (TAC→TGC)	pgpC ←	phosphatidylglycerophosphatase C, membrane bound

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,698,231	0	T	C	100.0%	61.5 / NA	18	Y107C (TAC→TGC)	pgpC	phosphatidylglycerophosphatase C, membrane bound
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/9); total (9/9)

CCACCATAGCCACGCTGAATTTGGCTGGCGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGTAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCACGAAATCGGCCTGCAACGTCTGTAAACGTGCTTCGCTGTGACCAAAAGTGCACCCCCACAGAAG  >  NC_000913/2698096‑2698355

ccaccaTAGCCACGCTGAATTTGGCTGGCGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAAcaggcagg                                                                                                                           >  1:203163/1‑139 (MQ=255)

        gCCACGCTGAATTTGGCTGGCGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAAt                                                                                                                   <  1:43073/139‑1 (MQ=255)

        gCCACGCTGAATTTGGCTGGCGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAAt                                                                                                                   <  2:583384/139‑1 (MQ=255)

        gCCACGCTGAATTTGGCTGGCGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAAt                                                                                                                   >  1:583384/1‑139 (MQ=255)

         ccACGCTGAATTTGGCTGGCGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAATc                                                                                                                  >  1:262730/1‑139 (MQ=255)

                           gcGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGCAggtgtt                                                                                                                       >  1:468887/1‑114 (MQ=255)

                           gcGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGCAggtggt                                                                                                                       <  2:468887/116‑1 (MQ=255)

                                                     gggCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAg                                                                      <  2:262730/139‑1 (MQ=255)

                                                                                            agagCCGGTAAGCAACCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCACGAAATCGGCCTGCAACGTCTGTAAACGTGCTTCg                               <  1:842049/139‑1 (MQ=255)

                                                                                                          aCCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAAt                                                                                                                   <  1:301316/41‑1 (MQ=255)

                                                                                                          aCCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAAt                                                                                                                   <  1:193272/41‑1 (MQ=255)

                                                                                                          aCCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAAt                                                                                                                   >  2:193272/1‑41 (MQ=255)

                                                                                                          aCCAGATATCAGCATCGGAACTTAACAGGCAGGTGGTTAAt                                                                                                                   >  2:301316/1‑41 (MQ=255)

                                                                                                                     gCATCGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCACGAAATCGGCCTGCAACGTCTGTAAACGTGCTTCGCTGTGACCAAAAGTGCACCCCcaca      >  2:108070/1‑139 (MQ=255)

                                                                                                                      cATCGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCACGAAATCGGCCTGCAACGTCTGTAAACGTGCTTCGCt                             <  2:624287/115‑1 (MQ=255)

                                                                                                                      cATCGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCACGAAATCGGCCTGCAACGTCTGTAAACGTGCTTCGCt                             >  1:624287/1‑115 (MQ=255)

                                                                                                                         cGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCa                                                                  >  2:447524/1‑75 (MQ=255)

                                                                                                                         cGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCa                                                                  <  1:447524/75‑1 (MQ=255)

                                                                                                                         cGGAACTTAACAGGCAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCACGAAATCGGCCTGCAACGTCTGTAAACGTGCTTCGCTGTGACCAAAAGTGCACCCCCACAGAAg  >  1:350883/1‑139 (MQ=255)

CCACCATAGCCACGCTGAATTTGGCTGGCGATAAGATTAACCCGCGGCAGCCAGGGCGTATCGAAATAAACCGCTTCAACCAGCGGCTGCGGAGAGCCGGTAATCAACCAGATATCAGCATCGGAACTTAACAGGTAGGTGGTTAATCGCTCCTGAACCAGCGGAAAGGCGGTAACATTGTCGCGAAACCAGCGCACGAAATCGGCCTGCAACGTCTGTAAACGTGCTTCGCTGTGACCAAAAGTGCACCCCCACAGAAG  >  NC_000913/2698096‑2698355

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A