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 F3 I95 R1	196	14.2	808436	96.0%	776098	85.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,626,268	A→G	pseudogene (359/1368 nt)	ydfJ ←	MHS family MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,626,268	0	A	G	100.0%	33.0 / NA	11	pseudogene (359/1368 nt)	ydfJ	MHS family MFS transporter
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (5/6); total (5/6)

GGCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCAAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGA  >  NZ_CP009273/1626184‑1626346

ggCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATg                                                                           >  1:240946/1‑90 (MQ=255)

                  aTCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATc                                                         <  2:213045/90‑1 (MQ=255)

                    cGTTCCGGCCCCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCtg                                                       <  1:123240/90‑1 (MQ=255)

                                       tCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAacaca                                    <  1:231852/90‑1 (MQ=255)

                                       tCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAacaca                                    <  2:78268/90‑1 (MQ=255)

                                                gCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAg                           <  1:205305/90‑1 (MQ=255)

                                                     cAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAggtggt                      >  2:319663/1‑90 (MQ=255)

                                                                 aataCGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCcat          >  2:109648/1‑90 (MQ=255)

                                                                  ataCGCAACGTCACCAGCGAGATGGGGGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCcatc         >  2:372553/1‑90 (MQ=255)

                                                                        aaCGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTg   <  1:243405/90‑1 (MQ=255)

                                                                         aCGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGa  >  2:69093/1‑90 (MQ=255)

GGCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCAAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGA  >  NZ_CP009273/1626184‑1626346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `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

CCGCGCTTACCTTTTGGCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCAAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAA  >  NZ_CP009273/1626169‑1626355

CCGCGCTTACCTTTTGGCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCG                                                                                         <  SRR3722235.269137/100‑1 (MQ=60)

CCGCGCTTACCTTTTGGCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCG                                                                                         <  SRR3722235.409662/100‑1 (MQ=60)

     CTTACCTTTTGGCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATG                                                                                    >  SRR3722235.244009/1‑100 (MQ=60)

                                   CGTTCCGGCCCCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTC                                                      <  SRR3722235.124661/100‑1 (MQ=60)

                                                      TCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGG                                   <  SRR3722235.234787/100‑1 (MQ=60)

                                                               GCACCCAACCCCTGAATAATACGCAACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGA                          <  SRR3722235.207824/100‑1 (MQ=60)

                                                                                       AACGTCACCAGCGAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAA  <  SRR3722235.246513/100‑1 (MQ=60)

CCGCGCTTACCTTTTGGCGCATATTCCGCCAGCATCGTACCGGCACCGGAAATTTCCGCACCTGCACCCAACCCCTGAATAATACGCAACGTCACCAGCAAGATGGGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAA  >  NZ_CP009273/1626169‑1626355

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`