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
A0 F0 I1 R1	61	39.0	4165548	97.4%	4057243	49.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	2,322,414	A→G	V93V (GTT→GTC)	ECW_RS11650 ←	head completion/stabilization protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	2,322,414	0	A	G	100.0%	10.9 / NA	9	V93V (GTT→GTC)	ECW_RS11650	head completion/stabilization protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (6/3); total (6/3)

GTAAAAAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGAACGTCCGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCGG  >  NC_017635/2322372‑2322459

gtaAAAAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTcag                                        >  1:480942/1‑48 (MQ=11)

    aaaaCTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTCAGCCAg                                    <  1:1638666/50‑1 (MQ=11)

     aaaCTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTCAGCCAGa                                   >  1:1129002/1‑50 (MQ=11)

     aaaCTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTCAGCCAGa                                   >  1:54801/1‑50 (MQ=11)

                       cGTCGATGCCGTCCGCCGGGACGTCAGCCAGACGCGAAAAACCGgcagc                  >  2:393141/1‑49 (MQ=17)

                            aTGCCGTCCGCCGGGACGTCAGCCAGACGCGAAAAACCGGCAGCAAtttt            >  1:1696912/1‑50 (MQ=17)

                                      ccgGGACGTCAGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCgg  <  1:1598699/50‑1 (MQ=14)

                                      ccgGGACGTCAGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCgg  <  2:1281420/50‑1 (MQ=14)

                                       cgGGACGTCAGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCgg  >  2:1382858/1‑49 (MQ=14)

GTAAAAAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGAACGTCCGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCGG  >  NC_017635/2322372‑2322459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GTAAAAAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGAACGTCCGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCGG  >  NC_017635/2322372‑2322459

GTAAAAAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTCAGC                                       >  M01420:85:000000000‑AC936:1:1107:9398:14782/1‑51 (MQ=12)

   AAAAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTCAGCCAG                                    <  M01420:85:000000000‑AC936:1:2109:10389:8189/51‑1 (MQ=12)

     AAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTCAGCCAGAC                                  >  M01420:85:000000000‑AC936:1:1101:15665:20633/1‑51 (MQ=12)

     AAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGGACGTCAGCCAGAC                                  >  M01420:85:000000000‑AC936:1:2102:27447:11151/1‑51 (MQ=12)

                            ATGCCGTCCGCCGGGACGTCAGCCAGACGCGAAAAACCGGCAGCAATTTTC           >  M01420:85:000000000‑AC936:1:2109:22631:27083/1‑51 (MQ=60)

                                     GCCGGGACGTCAGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCGG  <  M01420:85:000000000‑AC936:1:2108:10145:18631/51‑1 (MQ=60)

GTAAAAAACTTTGATGCTTTCACCGTCGATGCCGTCCGCCGGAACGTCCGCCAGACGCGAAAAACCGGCAGCAATTTTCTGTTCGCGG  >  NC_017635/2322372‑2322459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`