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
A1 F1 I1 R1	773	79.9	4112934	92.2%	3792125	104.5

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%	115.6 / NA	37	179 (TAG→TAA)	rcdA	transcriptional regulator of csgD and ybiJI, autoregulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (16/21); total (16/21)

AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGT  >  NC_000913/887826‑888088

aaCAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  1:381156/139‑1 (MQ=255)

aaCAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGAGGATGACGCTGAATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  2:1304404/139‑1 (MQ=255)

           gAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   <  2:1965944/139‑1 (MQ=255)

           gAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   <  1:1537620/139‑1 (MQ=255)

           gAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   <  2:1406661/139‑1 (MQ=255)

           gAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   >  1:1797179/1‑139 (MQ=255)

                 ggAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  2:98735/122‑1 (MQ=255)

                 ggAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              >  1:98735/1‑122 (MQ=255)

                 ggAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACaaa                                                                                                             >  1:911798/1‑139 (MQ=255)

                         ccgcGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                                                     <  1:571966/139‑1 (MQ=255)

                                                 ggggATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCgggg                                                                             <  2:629441/139‑1 (MQ=255)

                                                 ggggATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCgggg                                                                             <  2:646733/139‑1 (MQ=255)

                                                    gATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              >  2:1854798/1‑87 (MQ=255)

                                                    gATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  1:1854798/87‑1 (MQ=255)

                                                           cTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCt                                                                   <  2:911798/139‑1 (MQ=255)

                                                              cATTTTGTCACCGACCATAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTg                                                                          >  1:498956/1‑129 (MQ=255)

                                                              cATTTTGTCACCGACCATAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTg                                                                          <  2:498956/129‑1 (MQ=255)

                                                                               tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              >  1:1644252/1‑60 (MQ=255)

                                                                               tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  2:1644252/60‑1 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  2:1005642/53‑1 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              >  1:1005642/1‑53 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                                                     >  1:1589769/1‑78 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                                                     <  2:1589769/78‑1 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATg                                                                       >  2:1981620/1‑108 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATg                                                                       <  1:1981620/108‑1 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTcc                                                                 >  2:75901/1‑114 (MQ=255)

                                                                                      cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTcc                                                                 <  1:75901/114‑1 (MQ=255)

                                                                                            cgcgAGGAGATTTTTAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGa                                                                                       <  1:1338466/86‑1 (MQ=255)

                                                                                            cgcgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGa                                                                                       >  2:1338466/1‑86 (MQ=255)

                                                                                                 ggagATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   >  1:917726/1‑53 (MQ=255)

                                                                                                 ggagATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   <  2:917726/53‑1 (MQ=255)

                                                                                                       tttGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCTACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAGAGCAGTGGCACTAATTAAg                       >  1:1345687/1‑139 (MQ=255)

                                                                                                                        gggTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGaa      <  2:1797179/139‑1 (MQ=255)

                                                                                                                          gTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                                                     <  2:626821/42‑1 (MQ=255)

                                                                                                                          gTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                                                     >  1:626821/1‑42 (MQ=255)

                                                                                                                           ttGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAg   >  2:1461654/1‑139 (MQ=255)

                                                                                                                            tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAATCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGt  >  2:12553/1‑139 (MQ=255)

AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGT  >  NC_000913/887826‑888088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A