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 I230 R1	226	18.8	1048726	96.7%	1014118	86.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,012,918	A→G	D351G (GAC→GGC)	fliK →	flagellar hook‑length control protein FliK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,012,918	0	A	G	100.0%	25.2 / NA	9	D351G (GAC→GGC)	fliK	flagellar hook‑length control protein FliK
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (5/4); total (5/4)

TCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCA  >  NZ_CP009273/2012847‑2012999

tCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGt                                                                 >  1:85013/1‑90 (MQ=255)

                tCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACaa                                                 <  1:446342/90‑1 (MQ=255)

                tCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACaa                                                 <  2:117494/90‑1 (MQ=255)

                                    aCGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACaa                                                 <  1:163802/70‑1 (MQ=255)

                                    aCGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACaa                                                 >  2:163802/1‑70 (MQ=255)

                                          aGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGt                       >  1:37710/1‑90 (MQ=255)

                                           gCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGtt                      >  1:64101/1‑90 (MQ=255)

                                                         tctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTa        >  1:116396/1‑90 (MQ=255)

                                                               gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa  <  1:522500/90‑1 (MQ=255)

TCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCA  >  NZ_CP009273/2012847‑2012999

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CAACATCAGTGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC  >  NZ_CP009273/2012820‑2013009

CAACATCAGTGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGC                                                                                            >  SRR3722114.62564/1‑100 (MQ=60)

                 GCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGT                                                                           >  SRR3722114.85919/1‑100 (MQ=60)

                                           taagagacagAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAA                                                 <  SRR3722114.165430/90‑1 (MQ=60)

                                           TCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAA                                                 <  SRR3722114.451873/100‑1 (MQ=60)

                                                           GNCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGT                                 >  SRR3722114.38069/1‑100 (MQ=60)

                                                            CCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTT                                >  SRR3722114.64746/1‑100 (MQ=60)

                                                                          ACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTA                  >  SRR3722114.117630/1‑100 (MQ=60)

                                                                                          GGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC  <  SRR3722114.529043/100‑1 (MQ=60)

CAACATCAGTGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC  >  NZ_CP009273/2012820‑2013009

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`