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 F1 I1 R1	81	47.9	2225048	94.8%	2109345	113.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	593,467	T→G	D435A (GAC→GCC)	cusS ←	copper‑sensing histidine kinase in two‑component regulatory system with CusR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	593,467	0	T	G	100.0%	134.9 / NA	38	D435A (GAC→GCC)	cusS	copper‑sensing histidine kinase in two‑component regulatory system with CusR
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (19/19); total (19/19)

GCGGGTAATGTGATAACAAACCTTGTCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGTCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCACTACAATTGTCTCTCCGGTTG  >  NC_000913/593332‑593596

gCGGGTAATGTGATAACAAACCTTGTCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCaa                                                                                                                                <  2:319411/139‑1 (MQ=255)

          tgATAACAAACCTTGTCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGaa                                                                                                                      <  2:147642/139‑1 (MQ=255)

                   aCCTTGTCCCCCGCGCATCCGACGTTATCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTAACGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGAGATAGAAACGGCCaaa                                                                                                             >  1:1097223/1‑139 (MQ=255)

                   aCCTTGTCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCaaa                                                                                                             >  2:101988/1‑139 (MQ=255)

                   aCCTTGTCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCaaa                                                                                                             >  1:254154/1‑139 (MQ=255)

                    ccTTGTCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAAc                                                                                                            >  1:740061/1‑139 (MQ=255)

                         tCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCaa                                                                                                                                <  2:62573/114‑1 (MQ=255)

                         tCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCaa                                                                                                                                >  1:62573/1‑114 (MQ=255)

                         tCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATcg                                                                                                       >  2:681089/1‑139 (MQ=255)

                              cgcgCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTa                                                                                                  >  2:22290/1‑139 (MQ=255)

                                    tCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCt                                                                                            <  1:460708/139‑1 (MQ=255)

                                    tCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCt                                                                                            <  2:254154/139‑1 (MQ=255)

                                             aCCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCaa                                                                                   >  2:304601/1‑139 (MQ=255)

                                                         ccTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGt                                                                                                   <  1:160548/111‑1 (MQ=255)

                                                         ccTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGt                                                                                                   >  2:160548/1‑111 (MQ=255)

                                                              aTGTGCGACAACAATCGATTGCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCaa                                                                                                                                >  2:753808/1‑77 (MQ=255)

                                                              aTGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCaa                                                                                                                                <  1:753808/77‑1 (MQ=255)

                                                                    gACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTcgacg                                                            <  2:1047636/139‑1 (MQ=255)

                                                                     acaacaATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTcgacga                                                           <  2:636723/139‑1 (MQ=255)

                                                                        acaaTCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATaa                                                        <  1:749719/139‑1 (MQ=255)

                                                                                tttCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTcgacg                                                            >  1:189966/1‑127 (MQ=255)

                                                                                tttCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTcgacg                                                            <  2:189966/127‑1 (MQ=255)

                                                                                tttCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCAcc                                                <  2:529764/139‑1 (MQ=255)

                                                                                tttCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCAcc                                                >  1:529764/1‑139 (MQ=255)

                                                                                      tATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGa                                          >  1:156201/1‑139 (MQ=255)

                                                                                               gCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTc                                 >  2:28122/1‑139 (MQ=255)

                                                                                                    tACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACa                            <  1:28122/139‑1 (MQ=255)

                                                                                                         cTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAg                           >  2:766502/1‑135 (MQ=255)

                                                                                                         cTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAg                           <  1:766502/135‑1 (MQ=255)

                                                                                                         cTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCa                       >  1:335059/1‑139 (MQ=255)

                                                                                                         cTACCTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCa                       >  2:456444/1‑139 (MQ=255)

                                                                                                             cTTCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACTGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCACTAc                   <  2:1097223/139‑1 (MQ=255)

                                                                                                              ttCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGTGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGt                                            <  2:893000/113‑1 (MQ=255)

                                                                                                              ttCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGTGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGt                                            >  1:893000/1‑113 (MQ=255)

                                                                                                               tCACCTTTTCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCACTACaa                 <  1:101988/139‑1 (MQ=255)

                                                                                                                      ttCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCACTACAATTGtctc          >  1:775810/1‑139 (MQ=255)

                                                                                                                       tCGCTGGCGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCACTACAATTGtctct         <  1:681089/139‑1 (MQ=255)

                                                                                                                              cGGGAGGGGGCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCACTACAATTGTCTCTCCGGTTg  <  2:977207/139‑1 (MQ=255)

GCGGGTAATGTGATAACAAACCTTGTCCCCCGCGCATCCGACGTTACCGCAACCGTGCCTTTATGCGCGACAACAATCGATTTCACTATCGCCAGGCCAATACCGCTACCTTCACCTTTTCGCTGGCGGGAGGGGTCAACGCGATAGAAACGGTCAAACAATCGCGGTAAGTGCTCGGGCGCAATGGGCGTACCGGGGTTTTCGACGATAACTTGCACCAGGTGATCGACCGTCTGACAGCGCACTACAATTGTCTCTCCGGTTG  >  NC_000913/593332‑593596

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A