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 F4 I88 R1	217	30.5	1742422	95.9%	1670982	87.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	857,539	T→C	E175G (GAA→GGA)	ybiW ←	glycyl radical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	857,539	0	T	C	100.0%	78.0 / NA	22	E175G (GAA→GGA)	ybiW	glycyl radical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/4); total (18/4)

GCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAA  >  NZ_CP009273/857453‑857605

gCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCcag                                                                >  1:462256/1‑91 (MQ=255)

 cTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCACCAAGCCCTTTTCCcagc                                                               <  1:721874/91‑1 (MQ=255)

     ccGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCcagcagca                                                           >  2:112113/1‑91 (MQ=255)

               cTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAAtt                                                 >  1:134464/1‑91 (MQ=255)

               cTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAAtt                                                 >  2:631915/1‑91 (MQ=255)

               cTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAAtt                                                 >  1:430529/1‑91 (MQ=255)

                 tCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGTGGGAAATTCa                                               >  1:196424/1‑91 (MQ=255)

                 tCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCa                                               >  1:278659/1‑91 (MQ=255)

                        ccGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAg                                        >  2:7246/1‑91 (MQ=255)

                          gTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGt                                      >  1:522615/1‑91 (MQ=255)

                          gTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGt                                      >  2:533499/1‑91 (MQ=255)

                                 tGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATc                               >  2:810191/1‑91 (MQ=255)

                                  gATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCg                              >  2:786134/1‑91 (MQ=255)

                                    tGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGcc                            >  1:457090/1‑91 (MQ=255)

                                          agcgaCGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAggc                      >  1:822704/1‑90 (MQ=255)

                                          agcgaCGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGt                      <  1:858189/91‑1 (MQ=255)

                                                          ttCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCt      <  1:536548/91‑1 (MQ=255)

                                                           tCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTgcgc                                  >  1:167388/1‑62 (MQ=255)

                                                           tCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTgcgc                                  <  2:167388/62‑1 (MQ=255)

                                                           tCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCtt     >  2:194121/1‑91 (MQ=255)

                                                             cTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTa   >  2:722016/1‑91 (MQ=255)

                                                              tCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTaa  >  2:84123/1‑91 (MQ=255)

GCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAA  >  NZ_CP009273/857453‑857605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTC  >  NZ_CP009273/857443‑857611

TTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAG                                                                      >  SRR3722118.472006/1‑101 (MQ=60)

           CTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCACCAAGCCCTTTTCCCAGCAGCAGCGGGA                                                           <  SRR3722118.737719/101‑1 (MQ=60)

               CCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATT                                                       >  SRR3722118.137016/1‑101 (MQ=60)

               CCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATT                                                       >  SRR3722118.439606/1‑101 (MQ=60)

                 GTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGTGGGAAATTCA                                                     >  SRR3722118.200320/1‑101 (MQ=60)

                 GTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCA                                                     >  SRR3722118.284377/1‑101 (MQ=60)

                          TTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGT                                            >  SRR3722118.533698/1‑101 (MQ=60)

                                    GTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCC                                  >  SRR3722118.466722/1‑101 (MQ=60)

                                          ggtcTGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGC                            >  SRR3722118.840824/5‑101 (MQ=60)

                                                    AGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCT                  <  SRR3722118.877241/101‑1 (MQ=60)

                                                           TTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGctgtctcttatacacatct           >  SRR3722118.170670/1‑82 (MQ=60)

                                                                    TTCCTCGCGCAGACCATCAAGCCCTTTTCCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTC  <  SRR3722118.547928/101‑1 (MQ=60)

TTCAGGAATTGCTCACCGTGTAAATCTTCCAGCACCGTCAGGTTGATGCGCGAGCGACGTTCCGCTACTTCCTCGCGCAGACCATCAAGCCCTTTTTCCAGCAGCAGCGGGAAATTCACCGCCAGGTGCGCATCGCCGGAGGTCATATTGCCTTCCGCTTTAATGATTC  >  NZ_CP009273/857443‑857611

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`