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 F1 I1 R1	17	44.3	2973330	95.1%	2827636	75.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	4,162,470	A→C	T539P (ACC→CCC)	rpoB →	DNA‑directed RNA polymerase subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	4,162,470	0	A	C	100.0%	104.5 / NA	27	T539P (ACC→CCC)	rpoB	DNA‑directed RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (18/9); total (18/9)

TGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGA  >  REL606/4162399‑4162540

tGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCg                                                                    <  1:860636/76‑1 (MQ=255)

  gACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTg                                                                  <  2:1086438/76‑1 (MQ=255)

   aCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGa                                                                 >  1:1077574/1‑76 (MQ=255)

     cAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAAc                                                               >  2:736450/1‑76 (MQ=255)

     cAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCACACTCGGCCCAGGCGGTCTGCCACGTGAAc                                                               >  1:22914/1‑76 (MQ=255)

       gAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGt                                                             <  1:261766/76‑1 (MQ=255)

                   gTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGaa                                                 >  2:765534/1‑76 (MQ=255)

                   gTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGaa                                                 >  2:762241/1‑76 (MQ=255)

                   gTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGaa                                                 <  2:1288568/76‑1 (MQ=255)

                    tCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAg                                                >  2:291748/1‑76 (MQ=255)

                    ncTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAg                                                >  1:905359/2‑76 (MQ=255)

                     cTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGt                                               >  1:966259/1‑76 (MQ=255)

                        agaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCg                                            >  2:64739/1‑76 (MQ=255)

                        agaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCg                                            <  2:1053435/76‑1 (MQ=255)

                        agaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCg                                            >  2:157063/1‑76 (MQ=255)

                             aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACg                                       <  2:993551/76‑1 (MQ=255)

                                     aCGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCg                               <  2:183628/76‑1 (MQ=255)

                                        tcttATTTCCTCACTCGGCCCAGGCGGTCTGCCCCGTTAACGTTTATTCTTCGAAGTTCGAGACGTACACCCGACt                            >  2:326805/4‑76 (MQ=255)

                                         cgtATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTc                           >  1:1018693/1‑76 (MQ=255)

                                            aTCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACt                        >  1:955465/1‑76 (MQ=255)

                                               tcCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACg                     >  2:448387/1‑76 (MQ=255)

                                                   cACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTcg                 >  2:648528/1‑76 (MQ=255)

                                                      tCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGCCGTACACCCGACTCACTACGGTCGCGt              >  1:153750/1‑76 (MQ=255)

                                                      tCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGt              >  2:964485/1‑76 (MQ=255)

                                                        ggCCCGGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACAACGGTCGCGTAt            <  2:60527/76‑1 (MQ=255)

                                                        ggCCCAGGCGGTCTGCCGCGTGACCGTGCAGGCTTCGAANTTCGAGACGTACACCNGACTCACTACGGTCGCGTAt            >  2:1476800/1‑76 (MQ=255)

                                                                cGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATc    >  1:992038/1‑76 (MQ=255)

                                                                  gTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGa  <  1:420905/76‑1 (MQ=255)

TGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGA  >  REL606/4162399‑4162540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 28 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A