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
A27 F74 I0 R1	29	16.5	643684	90.6%	583177	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,196,204	G→A	53.8%	intergenic (‑105/+128)	thiC ← / ← rsd	phosphomethylpyrimidine synthase/regulator of sigma D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,196,204	0	G	A	53.8%	‑3.4 / 12.0	13	intergenic (‑105/+128)	thiC/rsd	phosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand): ref base G (2/4); new base A (4/3); total (6/7)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.43e-01

GGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGC  >  NC_000913/4196078‑4196337

gggTCTGTTTTGTTGCAGTCATCGCTCATTCCAAAAAGCTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGCTCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGAt                                                                                                                       <  2:909/143‑1 (MQ=255)

   tCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGCCGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCCGGTATTAGCCTGATCAg                                                                                                                    >  2:101994/1‑143 (MQ=255)

            ttgCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCGGGTATTAGCCTGAGCAGGTTCCGCgg                                                                                                           >  2:301119/1‑143 (MQ=255)

                    aTAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGaa                                                                                                   <  1:291330/143‑1 (MQ=255)

                       gCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaa                                                                                                <  1:96097/143‑1 (MQ=255)

                                aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGCCTCa                                                                                       >  1:115835/1‑143 (MQ=255)

                                          gtgcggggCTGGTCAGATGACGGATGGAGCAGGGTGCGGCAGCCCCACGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAg                                                                             <  2:140699/137‑1 (MQ=255)

                                                    tGTCAGACGACGGAGGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTGTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATGAACGGTCTCAGCCAGTGAAGGCGCTCCgct                                                                   >  2:151061/1‑141 (MQ=255)

                                                             acgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTa                                                          <  1:287000/143‑1 (MQ=255)

                                                                   gAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCg                                                    >  1:65806/1‑143 (MQ=255)

                                                                                    ccgcAGGGGCGATGCGTTCACAAAATAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                                   <  1:301119/143‑1 (MQ=255)

                                                                                        aGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGTTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTaa                               <  1:202336/143‑1 (MQ=255)

                                                                                                                     gTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGACAGTTACGGCAGTCCGACAAGAAATTAGCCCCGCAAATGGGGCCTTGAATGTAAATTACGCGTTACCAGCGCAGAAATCAAGc  >  1:213070/1‑143 (MQ=255)

GGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGC  >  NC_000913/4196078‑4196337

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A