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
A17 F109 I0 R1	32	27.2	584098	96.5%	563654	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,679,710	G→T	30.1%	G65V (GGC→GTC)	USA300HOU_2536 →	possible secretory antigen

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,679,710	0	G	T	30.1%	17.9 / 11.3	20	G65V (GGC→GTC)	USA300HOU_2536	possible secretory antigen
Reads supporting (aligned to +/- strand): ref base G (9/5); new base T (4/2); total (13/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.96e-01

CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAC  >  CP000730/2679584‑2679846

cTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAAt                                                                                                                             <  2:11355/140‑1 (MQ=255)

                    aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTaa                                                                                                         <  2:133223/140‑1 (MQ=255)

                         tCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCaa                                                                                                    >  2:153843/1‑140 (MQ=255)

                               gCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCAAAAAATTGGTATTACAATGCACGTAAACCAAAATATg                                                                                              >  2:243773/1‑140 (MQ=255)

                                cATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCAAAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATgg                                                                                             >  2:52475/1‑139 (MQ=255)

                                 aTGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGATAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAACCAAAATATGCg                                                                                            >  1:148754/1‑140 (MQ=255)

                                             attattATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGAAATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTaca                                                                                >  1:53838/1‑140 (MQ=255)

                                                     aGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGaaa                                                                        <  1:153843/140‑1 (MQ=255)

                                                        aaaaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAAtt                                                                     <  1:112568/140‑1 (MQ=255)

                                                               aaTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTCAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGCCGTACACCAAGAAAATTTGCAGTc                                                              >  1:79075/1‑140 (MQ=255)

                                                                           gggAATTTAAACGTCGCGCACAAGTCGGTAAACCTGGTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCAAGAAAAATAATAAAAAATACAATACGAACACCAAGAAAATTTGCTGTCATGCAATCAACt                                                  >  1:22402/1‑140 (MQ=255)

                                                                                 ttAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGa                                            >  1:82151/1‑140 (MQ=255)

                                                                                          gcgcACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAACATTTGATGTCATGCAATCAGCTGGAGGacatactagt                                   >  1:239994/1‑134 (MQ=255)

                                                                                            gcACAAGTCGGTAAACCTGTATCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACCTAATTCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATGTTATGGACa                                 >  2:281248/1‑140 (MQ=255)

                                                                                             cacaAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACAt                                >  1:142767/1‑140 (MQ=255)

                                                                                                aaGTCGGTAAACCTGTTTCTAATTGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc                             <  1:234551/140‑1 (MQ=255)

                                                                                                aaGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc                             <  1:29196/140‑1 (MQ=255)

                                                                                                         aaCCTGTTTCTAATAGATGGGGAAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgttgtt                    <  1:199925/140‑1 (MQ=255)

                                                                                                           ccTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGATGTCAAGCAATCAACTGCAGGAGATTATGGACATGTCGCAGTGGTTGa                  >  2:244667/1‑140 (MQ=255)

                                                                                                                  cTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGAATATTATGGACATGTCGCAGTAGTTAAACAAGta           >  2:271216/1‑140 (MQ=255)

                                                                                                                           ggggCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAc  <  1:273832/140‑1 (MQ=255)

CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAC  >  CP000730/2679584‑2679846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A