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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,169,693	C→T	pseudogene (475/475 nt)	gatR ←	pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,169,693	0	C	T	100.0%	107.9 / NA	34	pseudogene (475/475 nt)	gatR	pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (17/17); total (17/17)

GCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAA  >  NC_000913/2169572‑2169821

gcgttgTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAAttt                                                                                                                 <  1:1051601/139‑1 (MQ=255)

            accaccAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGtctt                                                                                                     >  2:1082170/1‑139 (MQ=255)

                ccaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGc                                                                                                 >  1:376033/1‑139 (MQ=255)

                ccaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGc                                                                                                 >  1:735364/1‑139 (MQ=255)

                    aTTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATg                                                                                             <  1:1008144/139‑1 (MQ=255)

                               ttGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                  <  1:1082170/139‑1 (MQ=255)

                                  cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                              <  1:259039/92‑1 (MQ=255)

                                  cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                              >  2:259039/1‑92 (MQ=255)

                                       aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGa                                                                          >  2:346728/1‑139 (MQ=255)

                                                 tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                <  2:376033/139‑1 (MQ=255)

                                                 tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                <  1:542288/139‑1 (MQ=255)

                                                     tctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                               >  2:955455/1‑136 (MQ=255)

                                                     tctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                               <  1:955455/136‑1 (MQ=255)

                                                               gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTaataataat                                                  >  1:119613/1‑139 (MQ=255)

                                                                           aaTGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTacac                                                                                                                             >  2:486948/1‑52 (MQ=255)

                                                                           aaTGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTacac                                                                                                                             <  1:486948/52‑1 (MQ=255)

                                                                               ccGGATGCGGTGTAGACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCcgc                                                                                                          <  1:750844/67‑1 (MQ=38)

                                                                               ccGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCcgc                                                                                                          >  2:750844/1‑67 (MQ=255)

                                                                                       ggTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTAc                          <  1:346728/139‑1 (MQ=255)

                                                                                                   ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                                    <  1:853654/69‑1 (MQ=255)

                                                                                                   ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                                    >  2:853654/1‑69 (MQ=255)

                                                                                                   ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                    >  2:257126/1‑117 (MQ=255)

                                                                                                   ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                    <  1:257126/117‑1 (MQ=255)

                                                                                                     aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                  >  1:670157/1‑53 (MQ=255)

                                                                                                     aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                  <  2:670157/53‑1 (MQ=255)

                                                                                                     aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACcgc            >  1:370848/1‑139 (MQ=255)

                                                                                                           cATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATg                                                                                             <  2:370800/52‑1 (MQ=255)

                                                                                                           cATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATg                                                                                             >  1:370800/1‑52 (MQ=255)

                                                                                                            aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                <  1:799776/80‑1 (MQ=255)

                                                                                                            aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                >  2:799776/1‑80 (MQ=255)

                                                                                                            aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGtt     <  2:370848/139‑1 (MQ=255)

                                                                                                              aCAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                    >  2:830059/1‑106 (MQ=255)

                                                                                                              aCAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                    <  1:830059/106‑1 (MQ=255)

                                                                                                               cAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTaaa  >  2:511851/1‑139 (MQ=255)

GCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAA  >  NC_000913/2169572‑2169821

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A