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 I195 R1	222	27.1	1551108	96.0%	1489063	86.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	510,152	Δ1 bp	coding (164/459 nt)	ybbJ ←	NfeD family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	510,151	0	C	.	90.0%	29.6 / ‑3.7	10	coding (165/459 nt)	ybbJ	NfeD family protein
Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (8/1); total (8/2)
Fisher's exact test for biased strand distribution p-value = 2.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAAT  >  NZ_CP009273/510064‑510224

gtgCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGcac                                                                         >  1:171074/1‑88 (MQ=255)

            gcgcACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGc                                                            >  2:509523/1‑90 (MQ=255)

                                     caccacAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCgg                                   >  2:184301/1‑90 (MQ=255)

                                        cacaGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTaa                                >  2:37299/1‑90 (MQ=255)

                                          caGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATc                              >  2:752983/1‑90 (MQ=255)

                                           aGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCa                             >  2:257311/1‑90 (MQ=255)

                                               aGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGc                         >  2:632196/1‑90 (MQ=255)

                                                  cggcgAGCAGCGTCAGGATGGCAAACATTCCCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGc                      <  1:632196/90‑1 (MQ=255)

                                                          agcGTCAGGAGGGCAAACATTCCCCCTT‑CCACCCCCACCCCAGCGGCACCAGCCAGACCCCCAGGCCGGTAATCACCGCTGCCAcgccgc              <  1:394545/90‑1 (MQ=255)

                                                                  gATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCacaac      >  2:314000/1‑90 (MQ=255)

                                                                      gCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAAt  >  1:20591/1‑90 (MQ=255)

GTGCTTTTGTTCGCGCACCCGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAAT  >  NZ_CP009273/510064‑510224

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 29 ≤` `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

CGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCT  >  NZ_CP009273/510114‑510245

CGGCGAGCAGCGTCAGGATGGCAAACATTCCCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTC                                 <  SRR3722073.645275/100‑1 (MQ=60)

        AGCGTCAGGAGGGCAAACATTCCCCCTT‑CCACCCCCACCCCAGCGGCACCAGCCAGACCCCCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAA                         <  SRR3722073.402953/100‑1 (MQ=60)

          CGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAAT                       >  SRR3722073.21115/1‑100 (MQ=60)

                        ACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC         >  SRR3722073.723934/1‑100 (MQ=60)

                               CCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCtgtctcttatacacatc  >  SRR3722073.134000/1‑83 (MQ=60)

CGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCT  >  NZ_CP009273/510114‑510245

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 10 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`