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	3,579,168	T→C	E339G (GAA→GGA)	ggt ←	gamma‑glutamyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,579,168	0	T	C	100.0%	40.2 / NA	14	E339G (GAA→GGA)	ggt	gamma‑glutamyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/6); total (8/6)

ATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTT  >  NZ_CP009273/3579084‑3579247

aTTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGAACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAg                                                                            <  2:30850/90‑1 (MQ=255)

     aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc                                                                       <  2:189089/90‑1 (MQ=255)

        ggCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggc                                                                    >  2:152401/1‑90 (MQ=255)

          cAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgt                                                                  >  1:108/1‑90 (MQ=255)

          cAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgt                                                                  <  1:98706/90‑1 (MQ=255)

                 tttGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgtaggcgta                                                           >  1:211477/1‑90 (MQ=255)

                              ttATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCt                                              >  1:179358/1‑90 (MQ=255)

                               tATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgt                                                                  <  1:323706/69‑1 (MQ=255)

                               tATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgt                                                                  >  2:323706/1‑69 (MQ=255)

                                    gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg                                        >  1:414741/1‑90 (MQ=255)

                                    gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg                                        >  2:79709/1‑90 (MQ=255)

                                        gcgcCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAttt                                    >  2:198859/1‑90 (MQ=255)

                                            cTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcat                                <  2:43036/90‑1 (MQ=255)

                                                                          gCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATttctt  <  2:380961/90‑1 (MQ=255)

ATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTT  >  NZ_CP009273/3579084‑3579247

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `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

ATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATG  >  NZ_CP009273/3579084‑3579209

ATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGT                            >  SRR3722113.109/1‑100 (MQ=60)

       CGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTA                     >  SRR3722113.213114/1‑100 (MQ=60)

          ataagagacaGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTT                  <  SRR3722113.326916/90‑1 (MQ=60)

          CAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTT                  <  SRR3722113.99595/100‑1 (MQ=60)

                    GGCACAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCT        >  SRR3722113.180778/1‑100 (MQ=60)

                          GGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATG  >  SRR3722113.419119/1‑100 (MQ=60)

ATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATG  >  NZ_CP009273/3579084‑3579209

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: `‑`