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	887,959	G→A	179 (TAG→TAA)	rcdA →	transcriptional regulator of csgD and ybiJI, autoregulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	887,959	0	G	A	100.0%	61.0 / NA	21	179 (TAG→TAA)	rcdA	transcriptional regulator of csgD and ybiJI, autoregulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (9/12); total (9/12)

CCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGT  >  NC_000913/887850‑888088

cccgcGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCa                                                                                                      >  2:587735/1‑139 (MQ=255)

                 tttATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAg                                                                                                                           <  1:287011/101‑1 (MQ=255)

                 tttATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAg                                                                                                                           >  2:287011/1‑101 (MQ=255)

                              tGACGCTGCATTTTGCCACCGACCGTAAGCCGCTATCGCGCGAGGGGATTTTGAGGATGGTTGAGAGGGTTGAATGGTAATAGATAAGTTTTAGATAACAAAAAAACCATCAACCTTGAACCGAAATGGCGGGGTTGAt                                                                        <  2:217112/139‑1 (MQ=255)

                                    tGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                                                     <  2:641088/104‑1 (MQ=255)

                                    tGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                                                     >  1:641088/1‑104 (MQ=255)

                                      cATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              >  1:469720/1‑77 (MQ=255)

                                      cATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  2:469720/77‑1 (MQ=255)

                                               accgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATggg                                                       <  1:350425/139‑1 (MQ=255)

                                               accgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATggg                                                       <  2:815481/139‑1 (MQ=255)

                                                              cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACAt                                                  >  1:89122/1‑129 (MQ=255)

                                                              cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACAt                                                  <  2:89122/129‑1 (MQ=255)

                                                                 tCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                     >  1:723109/1‑107 (MQ=255)

                                                                 tCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                     <  2:723109/107‑1 (MQ=255)

                                                                    ctcgAGGAGATTTTGAAGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAGAAACCCATCAACCTTGCACAGAAATGGCGGGGTTGATGGGCTCCGCATAATGGGGACATCAAAGGAAAGCAGTgg                                  <  2:769991/137‑1 (MQ=255)

                                                                                    ggATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGa                  <  1:587735/139‑1 (MQ=255)

                                                                                                    tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTg           >  2:367738/1‑130 (MQ=255)

                                                                                                    tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTg           <  1:367738/130‑1 (MQ=255)

                                                                                                    tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGt  >  2:631095/1‑139 (MQ=255)

                                                                                                         ggTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGaa      >  1:710674/1‑130 (MQ=255)

                                                                                                         ggTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGaa      <  2:710674/130‑1 (MQ=255)

CCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGT  >  NC_000913/887850‑888088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A