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
A1 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,298,108	T→A	intergenic (+4/‑232)	pnp → / → rnj2	Polyribonucleotide nucleotidyltransferase/Ribonuclease J 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,298,108	0	T	A	100.0%	86.0 / NA	26	intergenic (+4/‑232)	pnp/rnj2	Polyribonucleotide nucleotidyltransferase/Ribonuclease J 2
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (11/15); total (11/15)

ACATTTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCTGTAT  >  USA300TCH1516_ALE/1297968‑1298245

acaTTTCACAAATTTCAAAAAATATAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTc                                                                                                                                    <  3:111215/148‑1 (MQ=255)

  aTTTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCat                                                                                                                                  <  3:69343/148‑1 (MQ=255)

        caAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgacg                                                                                                                            >  4:276827/1‑148 (MQ=255)

              tCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgac                                                                                                                             >  1:48851/1‑141 (MQ=255)

                                        aGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCa                                                                                            >  4:387384/1‑148 (MQ=255)

                                                      tCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTg                                                                              >  3:131195/1‑148 (MQ=255)

                                                      tCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTg                                                                              >  3:131200/1‑148 (MQ=255)

                                                           gACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAg                                                                                <  2:39358/141‑1 (MQ=255)

                                                                  agtaaGTTAAAATTACAGAAATTGATAAACAAGGTTGAGTAAATCCTTCACAAAGAACATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCg                                                                         <  2:39974/138‑1 (MQ=255)

                                                                   tGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGGAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGt                                                                        <  2:35189/141‑1 (MQ=255)

                                                                                             aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATATTAGATAACGTCATATGATGACAATGGATCGTCATGTGATTTTTTTATGCCACTTCTTACGATGTGACCCGTTTTGAATTTGTTGTATTGTACATTTTaatccgc                                       <  4:97796/148‑6 (MQ=255)

                                                                                             aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGc                                       <  3:259472/148‑1 (MQ=255)

                                                                                             aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGc                                       <  3:130921/148‑1 (MQ=255)

                                                                                                aaGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCttt                                    >  4:404153/1‑148 (MQ=255)

                                                                                                    tCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTttatta                                <  3:412983/148‑1 (MQ=255)

                                                                                                               cTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTTTGTTTTTTTTTACGAAGTGACCCGTTTTGTATTTGTTGTATTGAACATTTTAAAACGCTTTCTTATTTTGTGTGCa                     >  4:237226/1‑148 (MQ=255)

                                                                                                                  cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACt                  >  3:328181/1‑148 (MQ=255)

                                                                                                                  cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACt                  >  3:72437/1‑148 (MQ=255)

                                                                                                                  cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACt                  >  3:79338/1‑148 (MQ=255)

                                                                                                                     aTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGc                      <  1:39094/141‑1 (MQ=255)

                                                                                                                             ttAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATcc       <  3:404153/148‑1 (MQ=255)

                                                                                                                             ttAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATcc       <  3:227685/148‑1 (MQ=255)

                                                                                                                               agaagaATAATATATAAAGTCAGATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTTAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCtg     <  4:247245/148‑1 (MQ=255)

                                                                                                                                gaagaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAAtt           <  2:48851/141‑1 (MQ=255)

                                                                                                                                gaagaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCtgt    <  3:276827/148‑1 (MQ=255)

                                                                                                                                  agaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTTACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTTTGTGCAACTGTTAATTATCCtgtat  >  4:240820/1‑148 (MQ=255)

ACATTTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTATCCTGTAT  >  USA300TCH1516_ALE/1297968‑1298245

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

GATK/CNVnator alignment

N/A