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
A13 F63 I0 R1	31	53.1	1128482	96.8%	1092370	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,143,110	G→A	51.0%	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	51.0%	‑0.7 / 43.5	33	V163V (GTG→GTA)	USA300HOU_2026	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base G (9/7); new base A (9/8); total (18/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.40e-01

AAAGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCTGTTCCAAT  >  CP000730/2142972‑2143250

aaaGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGc                                                                                                                                            >  2:300624/1‑141 (MQ=255)

          attattGCTCGAAAAATACCTATATTTATCTTCTTTGTCTCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAAGCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTattatt                                                                                                                                  <  1:414897/141‑1 (MQ=255)

                 cTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTacaa                                                                                                                           <  1:9678/141‑1 (MQ=255)

                     aaaaaTACCTATATTTATCTTCTTTGTATATATTATTGGTCATTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGt                                                                                                                       >  2:222511/1‑141 (MQ=255)

                         aTACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGt                                                                                                                   <  1:330018/141‑1 (MQ=255)

                           aCCTATATTTATCTTATTTGTATCTATTATTGGTCCTTTGTTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTc                                                                                                                 >  1:186022/1‑141 (MQ=255)

                                          tttttgagcTATTATCGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTACCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCAtt                                                                                                  <  2:133881/133‑1 (MQ=255)

                                           tttGTATCTATTATTGGTCCTTTCTTAGAAGAATGTGTATTCAGAAAAGTAATCTTTGGAAAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCTTTTGTTATTGCTACAACTGTAAGTTCATTAATATTTGccgta                                                                                                 >  1:6257/1‑137 (MQ=255)

                                           taggTAGCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCCTTa                                                                                                 >  2:95223/4‑141 (MQ=255)

                                              gTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGca                                                                                              <  2:551717/141‑1 (MQ=255)

                                              gTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTCTGGTGGCTGAAGTAAGTCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGca                                                                                              <  1:552491/141‑1 (MQ=255)

                                                 tCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACCACAGTACGTTCATTAATATTTGCATTAGcacaa                                                                                           >  2:208359/1‑140 (MQ=255)

                                                 tCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAgacaat                                                                                           >  1:262065/1‑136 (MQ=255)

                                                  cTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATa                                                                                          >  1:355114/1‑141 (MQ=255)

                                                        ttGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGAtt                                                                                    <  1:43982/141‑1 (MQ=255)

                                                            tCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCaa                                                                                <  1:541299/141‑1 (MQ=255)

                                                            tCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCaa                                                                                >  1:188111/1‑141 (MQ=255)

                                                             ccTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCTATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCaaa                                                                               >  1:132000/1‑141 (MQ=255)

                                                                ttattaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAAttt                                                                            >  2:387164/1‑141 (MQ=255)

                                                                ttattaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAAttt                                                                            >  2:386678/1‑141 (MQ=255)

                                                                ttaatcgaagaaCAAGTATTCGACAACGTAATCTTTGGAGAATTATTTAATGCGATGAAAGGTAATCGTATCGTAGCATTTATTAGTGCTACAACAGTAAGTTCATTAATAGTTGCATTAGCACATAATGATTTCAAAttt                                                                            <  1:126262/135‑1 (MQ=255)

                                                                   taagaagaagaTGTATTCAGAAAGGTAATCTTTTGAGAATTATTTAAGGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTAtt                                                                         <  2:89258/139‑1 (MQ=255)

                                                                     agaagaATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTACCACATAATGATTTCAAATTTATTcc                                                                       >  2:153345/1‑141 (MQ=255)

                                                                           atatGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTa                                                                 <  1:112042/141‑1 (MQ=255)

                                                                               gTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAGTTTCTTCCAGTTTAttgt                                                             >  2:44289/1‑139 (MQ=255)

                                                                                       aaaaGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATggg                                                     <  1:222511/141‑1 (MQ=255)

                                                                                         aaGTAATTTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGgtg                                                   <  2:104739/141‑1 (MQ=255)

                                                                                          aGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGgtgt                                                  >  2:399799/1‑141 (MQ=255)

                                                                                                    ggAGAATTATTTAATGCGATTAAAAGTAATCGGATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATATTGATTTCAAATTTATCCCGGTGTATTTTGGTATAGGGGTCGTTTTTTct                                        >  1:92998/1‑140 (MQ=255)

                                                                                                                             gTAATCGTATCGTGGCATTTATTATGGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGc               <  1:150421/141‑1 (MQ=255)

                                                                                                                              tAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGAGTAATTTTTTAATGCGAATATGTATGGACAAACCCGCt              >  2:384931/1‑141 (MQ=255)

                                                                                                                               aaTCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCtt             <  2:355114/141‑1 (MQ=255)

                                                                                                                               aaTCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCtt             >  2:448543/1‑141 (MQ=255)

                                                                                                                                          ggCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAAAGGCTTGCTGTTCCAat  >  2:455032/1‑141 (MQ=255)

AAAGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCTGTTCCAAT  >  CP000730/2142972‑2143250

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