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 F1 I2 R1	65	21.2	1002576	96.5%	967485	111.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,811	Δ1 bp	intergenic (‑43/+23)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,811	0	C	.	100.0%	71.1 / NA	17	intergenic (‑43/+23)	pyrE/rph	orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (8/9); total (8/9)

AAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCC  >  NC_000913/3815730‑3815941

aaGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAt                                                                          <  2:274958/139‑1 (MQ=255)

   cgcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGga                                                                       >  2:196177/1‑139 (MQ=255)

                    ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGc                                                      <  1:308682/139‑1 (MQ=255)

                            tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCca                                              <  1:313960/139‑1 (MQ=255)

                                     aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGa                                     >  1:217545/1‑139 (MQ=255)

                                      tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                    <  2:217545/139‑1 (MQ=255)

                                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTc                                                                                                                        >  2:83814/1‑50 (MQ=255)

                                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTc                                                                                                                        <  1:83814/50‑1 (MQ=255)

                                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTg                                                                                      >  1:55427/1‑84 (MQ=255)

                                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTg                                                                                      <  2:55427/84‑1 (MQ=255)

                                               tcctcATCTTACTTTTCTACAGACAAAAAAATGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCATCGCGACAATAGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                    <  2:335923/130‑1 (MQ=255)

                                               tcctcATCTTACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCATCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAg                                    >  1:335923/1‑130 (MQ=255)

                                                       ttACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGcgcc                                                                                              >  1:437/1‑64 (MQ=255)

                                                       ttACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGcgcc                                                                                              <  2:437/64‑1 (MQ=255)

                                                        tACTTTTCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                  >  2:422483/1‑139 (MQ=255)

                                                              tCTACAGACAAAAAAAAGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc            >  1:311546/1‑139 (MQ=255)

                                                                        aaaaaaaGG‑GACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTCCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAAGGCTCGCCTTCTGcc  <  1:334867/139‑1 (MQ=255)

AAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCC  >  NC_000913/3815730‑3815941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A