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
A15 F18 I0 R1	80	28.1	641476	93.5%	599780	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,143,110	G→A	40.3%	V163V (GTG→GTA)	USA300HOU_2026 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,143,110	0	G	A	40.3%	3.5 / 17.4	20	V163V (GTG→GTA)	USA300HOU_2026	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base G (7/5); new base A (4/4); total (11/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.44e-01

CTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCT  >  CP000730/2142976‑2143242

cTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCAtt                                                                                                                                 >  2:277158/1‑140 (MQ=255)

               cGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTGAGAAAAGTAATCTTTGAAGAATTTTTTAATGTGATTAAAGATAATAGTATCGTGGTATTTATTATTGCTgcaat                                                                                                                  <  2:187436/140‑2 (MQ=255)

                  aaaaTACCTATGTTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAATGTAATCGTATCGTAGCATTTATTATTGCTACAACAGt                                                                                                               <  2:135041/140‑1 (MQ=255)

                  aaaaTACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATCATTGCTACAACAGt                                                                                                               <  1:176205/140‑1 (MQ=255)

                          tataTTTATCTTCTTTGTATCTCTTATTGGTCCTTTATTAGAAGAATATGTCTTCAGAAAAGTAATATTTGAAGAATTATTTAATGCGATTCAAGGTAATCGTATCGTGGCTTTTATCTTTGGTTAAACAGTAAGTTCAt                                                                                                       >  2:167413/1‑140 (MQ=255)

                          tataTTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCAt                                                                                                       >  2:264077/1‑140 (MQ=255)

                                   cttcttTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTg                                                                                              >  1:38917/1‑140 (MQ=255)

                                     tcttTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCa                                                                                            <  2:293195/140‑1 (MQ=255)

                                                              attaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTa                                                                   >  2:78880/1‑140 (MQ=255)

                                                                 agaagaATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATCATTTCAAATTTATTc                                                                >  1:253516/1‑140 (MQ=255)

                                                                    agaaTATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAg                                                             <  1:277158/140‑1 (MQ=255)

                                                                    agaaTATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAg                                                             <  1:110086/140‑1 (MQ=255)

                                                                            tagtCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATGGCTACAACAGTAAGGTCATTAATAGTTGAATTAGCACCTAATGATTTCAAATTTATTCCATTTGAtttt                                                     >  2:151994/4‑140 (MQ=255)

                                                                                              ttGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCAttttt                                   >  2:245199/1‑140 (MQ=255)

                                                                                                    aaTTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTCCTATAACTGTATGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTa                             >  2:36458/1‑140 (MQ=255)

                                                                                                         tttAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCata                        <  1:287411/140‑1 (MQ=255)

                                                                                                               gCGATGAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTAATTAGCATATGtttt                  >  2:179753/1‑139 (MQ=255)

                                                                                                                   ttAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACa              >  2:275926/1‑140 (MQ=255)

                                                                                                                               gtatcgtGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCt  <  1:167413/140‑1 (MQ=255)

                                                                                                                               gtatcgtGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCt  <  1:264077/140‑1 (MQ=255)

CTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCT  >  CP000730/2142976‑2143242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A