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
A7 F57 I0 R1	50	10.6	235668	93.0%	219171	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	512,643	A→G	58.8%	intergenic (+711/‑150)	recR → / → rrs1	recombination protein RecR/16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	512,643	0	A	G	58.8%	4.8 / 16.0	17	intergenic (+711/‑150)	recR/rrs1	recombination protein RecR/16S ribosomal RNA
Reads supporting (aligned to +/- strand): ref base A (3/4); new base G (6/4); total (9/8)
Fisher's exact test for biased strand distribution p-value = 6.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01

GTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAAT  >  CP000730/512505‑512771

gtgtAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTtaat                                                                                                                                >  2:105738/1‑141 (MQ=255)

                    gtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCtt                                                                                                            <  1:13120‑M1/46‑1 (MQ=255)

                                        cgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACa                                                                                        <  2:12073‑M1/66‑1 (MQ=255)

                                                         ggCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACa                                                                       <  1:105738/141‑1 (MQ=255)

                                                            ttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAata                                                                    >  1:11394‑M1/56‑141 (MQ=255)

                                                                              tAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCaa                                                  <  1:89018/141‑1 (MQ=255)

                                                                                    aTAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACg                                            <  2:56388/141‑1 (MQ=255)

                                                                                           aaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACtat                                     >  1:63267‑M1/25‑141 (MQ=255)

                                                                                                             aattTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTAttt                   >  2:32595/1‑141 (MQ=255)

                                                                                                               ttttAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAg                 <  2:5757/141‑1 (MQ=255)

                                                                                                               ataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGTTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTACAAAAAACGTAACTATAAGTTACAAACATTATTTAg                 >  2:104565‑M1/5‑141 (MQ=255)

                                                                                                               ataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAg                 <  2:46978‑M1/137‑1 (MQ=255)

                                                                                                                taaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGt                >  2:13120‑M1/4‑141 (MQ=255)

                                                                                                                        gTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGa        >  2:57027/1‑141 (MQ=255)

                                                                                                                         ttATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTAATGAg       >  1:68486/1‑141 (MQ=255)

                                                                                                                          tATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGc      >  1:38896/1‑141 (MQ=255)

                                                                                                                          tATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGc      >  1:16926/1‑141 (MQ=255)

                                                                                                                              gACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAAt  <  1:26848/141‑1 (MQ=255)

GTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTATTTAGTATTTATGAGCTAAT  >  CP000730/512505‑512771

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A