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 F2 I229 R1	214	17.4	943020	97.5%	919444	87.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	539,975	A→G	D258D (GAT→GAC)	allC ←	allantoate deiminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	539,975	0	A	G	100.0%	42.7 / NA	15	D258D (GAT→GAC)	allC	allantoate deiminase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/6); total (9/6)

GAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT  >  NZ_CP009273/539900‑540061

gAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCtttt                                                                          >  2:347974/1‑90 (MQ=255)

                 gCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACt                                                         >  2:164318/1‑90 (MQ=255)

                       caTTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGc                                                   >  2:137218/1‑90 (MQ=255)

                           tACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAAt                                               >  1:157833/1‑90 (MQ=255)

                              cGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCg                                            >  2:164669/1‑90 (MQ=255)

                                 aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACt                                         >  1:187618/1‑90 (MQ=255)

                                 aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACt                                         >  1:81839/1‑90 (MQ=255)

                                     gggCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGaaa                                     <  2:157833/90‑1 (MQ=255)

                                     gggCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGaaa                                     <  2:251337/90‑1 (MQ=255)

                                                     tGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac                     >  2:151655/1‑90 (MQ=255)

                                                     tGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac                     <  2:327466/90‑1 (MQ=255)

                                                      gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  2:14621/1‑90 (MQ=255)

                                                                        cGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCgt  <  1:462730/90‑1 (MQ=255)

                                                                        cGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCgt  <  2:159459/90‑1 (MQ=255)

                                                                        cGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCgt  <  2:56451/90‑1 (MQ=255)

GAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT  >  NZ_CP009273/539900‑540061

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

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCAT  >  NZ_CP009273/539917‑540072

GCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAAT                                                          >  SRR3722113.159137/1‑100 (MQ=60)

      CATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACT                                                    >  SRR3722113.189091/1‑100 (MQ=60)

      CATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACT                                                    >  SRR3722113.82556/1‑100 (MQ=60)

                                                       CGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCA   <  SRR3722113.467620/100‑1 (MQ=60)

                                                        GGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCAT  <  SRR3722113.165658/100‑1 (MQ=60)

                                                        GGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCAT  >  SRR3722113.394961/1‑100 (MQ=60)

GCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGTGGTGCCTGCAT  >  NZ_CP009273/539917‑540072

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`