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 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

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%	86.4 / NA	28	179 (TAG→TAA)	rcdA	transcriptional regulator of csgD and ybiJI, autoregulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (12/16); total (12/16)

CGAACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGTTCTG  >  NC_000913/887824‑888092

cGAACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGtaatag                                                                                                                                    >  1:772739/1‑139 (MQ=255)

  aaCAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                                  <  2:772739/139‑1 (MQ=255)

       tGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGtt                                                                                                                             >  2:20421/1‑139 (MQ=255)

               aCCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATaa                                                                                                                     >  1:259035/1‑139 (MQ=255)

               aCCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATaa                                                                                                                     >  2:733264/1‑139 (MQ=255)

               aCCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATaa                                                                                                                     >  2:608310/1‑139 (MQ=255)

               aCCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATaa                                                                                                                     >  1:975635/1‑139 (MQ=255)

                          cccgcGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                                  >  2:739505/1‑115 (MQ=255)

                          cccgcGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                                  <  1:739505/115‑1 (MQ=255)

                                             tATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATg                                                                                       >  2:624952/1‑139 (MQ=255)

                                                tGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCg                                                                                    <  1:608310/139‑1 (MQ=255)

                                                tGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCg                                                                                    <  1:733264/139‑1 (MQ=255)

                                                 gAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCgg                                                                                   <  2:259035/139‑1 (MQ=255)

                                                    gggATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGt                                                                                >  2:850442/1‑139 (MQ=255)

                                                       aTGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGa                                                                             >  1:159881/1‑139 (MQ=255)

                                                        tGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGAt                                                                            <  1:137995/139‑1 (MQ=255)

                                                                         accgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGTTAATAGATAAGTTTTAGATAACAAAAACCCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATggg                                                           <  1:813693/139‑1 (MQ=255)

                                                                         accgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATggg                                                           <  1:850442/139‑1 (MQ=255)

                                                                         accgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATggg                                                           <  2:499534/139‑1 (MQ=255)

                                                                           cgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGa                                                         <  1:361273/139‑1 (MQ=255)

                                                                                                cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                    <  1:20421/139‑1 (MQ=255)

                                                                                                   ggagATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                    <  2:401448/136‑1 (MQ=255)

                                                                                                   ggagATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                    >  1:401448/1‑136 (MQ=255)

                                                                                                      gaTTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAAtt                              <  2:267087/139‑1 (MQ=255)

                                                                                                                              tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                         >  2:98652/1‑72 (MQ=255)

                                                                                                                              tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                         <  1:98652/72‑1 (MQ=255)

                                                                                                                              tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGaaa                                              >  2:756898/1‑99 (MQ=255)

                                                                                                                              tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGaaa                                              <  1:756898/99‑1 (MQ=255)

                                                                                                                                  gggTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGTTCTg  <  2:975635/139‑1 (MQ=255)

CGAACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGTTCTG  >  NC_000913/887824‑888092

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A