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
A19 F166 I0 R1	50	63.8	1389156	94.9%	1318309	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,539,250	C→G	100%	intergenic (‑349/+37)	aroC ← / ← USA300HOU_1405	chorismate synthase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,539,250	0	C	G	100.0%	89.1 / ‑6.5	32	intergenic (‑349/+37)	aroC/USA300HOU_1405	chorismate synthase/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base G (20/11); minor base A (0/1); total (20/12)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGT  >  CP000730/1539115‑1539385

ttGCATCATATGCTCGTTATTTAACAGTGATTAGCCGTTTTGATATTCTCGTTGCGCAACTTTATCAAATGGTATACTTACTGCATTTCTTTGTATAAAGGAATGAACTGTTAATTATTAATAAAGTTAATCAGTGAGttt                                                                                                                                    <  2:577070/141‑1 (MQ=255)

ttGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGttt                                                                                                                                    <  2:691408/141‑1 (MQ=255)

    atcatATAATCATTAATTAAAAATGATTAGACGTTTTAATATAATCGTATCGCAACTTTAGCAAAGAATATACTGACTACATTTCTTAATACAAAGGAACGAACTGTTAATTATTAATAAAGTTAATAAATGCGTTGaaaa                                                                                                                                >  2:295826/1‑141 (MQ=255)

     tcatATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATCAATAAAGGTAATCAGTGAGTATaaaaa                                                                                                                               >  2:142476/1‑141 (MQ=255)

      catATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTaaaaaa                                                                                                                              <  1:458172/141‑1 (MQ=255)

                        aaaTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAatat                                                                                                            >  1:156042/1‑141 (MQ=255)

                        aaaTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAatat                                                                                                            >  1:129803/1‑141 (MQ=255)

                        aaaTGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAataa                                                                                                            >  2:196346/1‑140 (MQ=255)

                                          atatAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATAAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCttt                                                                                          >  2:432935/1‑141 (MQ=255)

                                              aaTCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGtt                                                                                      <  1:93371/141‑1 (MQ=255)

                                                    aTCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAGCGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATAAGTTAAGCGCTTTTGTTATACtt                                                                                >  2:554950/1‑141 (MQ=255)

                                                      cGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGACCTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTAATACTTTg                                                                              >  2:271337/1‑141 (MQ=255)

                                                      cGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTATGCGCTTTTATTATACTTTg                                                                              >  2:363679/1‑141 (MQ=255)

                                                              tAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCaaa                                                                      >  2:556683/1‑141 (MQ=255)

                                                                acAAATAATAAACTGACTACATTTATTAATACAAAAGAACGAACTGTTAATTATTAATAATGTTAATCAGAAAGAAAAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCaaaaa                                                                    <  2:276038/140‑1 (MQ=255)

                                                                 aaaaTAACATACTTACTACATTTCTTAATACAAAAGAACGAACTCTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAat                                                                   <  2:272299/140‑1 (MQ=255)

                                                                     taataTACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATaa                                                               >  1:548072/1‑141 (MQ=255)

                                                                                 tACATTGCTTAATACAAAAGTACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGCTTAAAAAAATTATTATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTa                                                   <  2:418559/141‑1 (MQ=255)

                                                                                 tACAATTATTAATACGAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCATTTAAAAAAATTATGATATGAAAATATACATATGTTAAGCTCTTTTGTTATACTTTGACTTCAAAAATATATTCAATTCTTTTa                                                   <  2:225182/141‑1 (MQ=255)

                                                                                     tttCTTAATACAAAAGAACGAACTGCTAATTATTAATAAAGTTAATCAGTGCGGTTAAAAAAATTATGATATTAAAAAATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAAAATAATCAATTCTTTCACTaa                                               >  2:104199/1‑141 (MQ=255)

                                                                                         ttAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACa                                           >  2:586276/1‑141 (MQ=255)

                                                                                                aaaaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATaaaaaa                                    <  1:597535/141‑1 (MQ=255)

                                                                                                  aaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAata                                  >  1:123476/1‑141 (MQ=255)

                                                                                                  aaGAACGAACTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAata                                  >  1:431036/1‑141 (MQ=255)

                                                                                                      acgaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATaaa                              >  1:205993/1‑141 (MQ=255)

                                                                                                        gaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAAta                            >  1:154780/1‑140 (MQ=255)

                                                                                                        gaacTGTTAATTATTAATAAAGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATAAACAAATGTTAAGCGCTTTTGTTATACTTTGACTTCAACAATAAAATCACTTCTTTTACTACTACATAATAGATATAAATg                            >  1:662275/1‑141 (MQ=255)

                                                                                                                          aaaGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATAATTTAAAATAAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAaata          <  2:156042/141‑1 (MQ=255)

                                                                                                                          aaaGTTAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTCAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAaata          >  2:163274/1‑141 (MQ=255)

                                                                                                                              ttAATCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTCAGCGCTTCTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAAttt      <  1:512021/141‑1 (MQ=255)

                                                                                                                                  tCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGt  <  1:586276/141‑1 (MQ=255)

                                                                                                                                  tCAGTGCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGt  >  2:275931/1‑141 (MQ=255)

TTGCATCATATAATCATTAATTAAAAATGATTAGCCGTTTTAATATAATCGTATCGCAACTTTAGCAAATAATATACTGACTACATTTCTTAATACAAAAGAACGAACTGTTAATTATTAATAAAGTTAATCAGTCCGTTTAAAAAAATTATGATATTAAAATATACATATGTTAAGCGCTTTTGTTATACTTTGACTTCAAAAATATAATCAATTCTTTTACTAATACATAAAAAATATAAATGAGAGTCAGTATAAAAATAATTTTTGT  >  CP000730/1539115‑1539385

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