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
A12 F1 I1 R1	760	58.2	3022526	90.8%	2744453	102.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,618,218	G→A	397 (TAG→TAA)	ydeA →	arabinose efflux transporter, arabinose‑inducible

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,618,218	0	G	A	100.0%	120.9 / NA	38	397 (TAG→TAA)	ydeA	arabinose efflux transporter, arabinose‑inducible
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (18/20); total (18/20)

TGAGTTTGCACTGGTCAATGTCGATGATTGGTTATGTGGGCGCGGTGCCTGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAGTTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACCAGCAGGAATCCCATCAGACGGGAGATCGCTTCAATGCCAC  >  NC_000913/1618094‑1618346

tGAGTTTGCACTGGTCAATGTCGATGATTGGTTATGTGGGCGCGGTGCCTGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCAtt                                                                                                                    <  1:575088/139‑1 (MQ=255)

   gTTTGCACTGGTCAATGTCGATGATTGGTTATGTGGGCGCGGTGCCTGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCgg                                                                                                                 <  2:515131/139‑1 (MQ=255)

                               ttATGTGGGCGCGGTGCCTGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGAt                                                                                     >  1:1139341/1‑139 (MQ=255)

                                      ggCGCGGTGCCTGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAACGATTTCCAgg                                                                              >  1:1010551/1‑139 (MQ=255)

                                                 tGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGa                                                                                                                              <  2:165983/80‑1 (MQ=255)

                                                 tGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGa                                                                                                                              >  1:165983/1‑80 (MQ=255)

                                                       tGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTa                                                                                                 <  2:999961/103‑1 (MQ=255)

                                                       tGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTa                                                                                                 >  1:999961/1‑103 (MQ=255)

                                                          cgcgTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTg                                                          <  2:1139341/139‑1 (MQ=255)

                                                          cgcgTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAACGATTTCCAGGATGCCGTTAATAATAAACTg                                                          <  2:1010551/139‑1 (MQ=255)

                                                                           tCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACca                                         >  2:336787/1‑139 (MQ=255)

                                                                                 tatTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCcatacat                                             <  1:1155246/129‑1 (MQ=255)

                                                                                 tatTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCcatacat                                             >  2:1155246/1‑129 (MQ=255)

                                                                                      cgccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATg                                                                           >  2:838178/1‑94 (MQ=255)

                                                                                      cgccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATg                                                                           <  1:838178/94‑1 (MQ=255)

                                                                                      cgccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTg                                                          <  1:1287323/111‑1 (MQ=255)

                                                                                      cgccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTg                                                          >  2:1287323/1‑111 (MQ=255)

                                                                                       gccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAgg                                                                              <  1:227704/90‑1 (MQ=255)

                                                                                       gccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAgg                                                                              >  2:227704/1‑90 (MQ=255)

                                                                                        ccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCacac                                                     <  2:573795/114‑1 (MQ=255)

                                                                                        ccgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCacac                                                     >  1:573795/1‑114 (MQ=255)

                                                                                         cgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCggg                                                                                                                <  2:1097316/54‑1 (MQ=255)

                                                                                         cgcTGGCCAGTGACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCggg                                                                                                                >  1:1097316/1‑54 (MQ=255)

                                                                                                    gACACTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACCAGCAGGAATCCCATCAGACGGGAGAt                <  1:336787/139‑1 (MQ=255)

                                                                                                     acacTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATg                                                                           >  2:1003587/1‑79 (MQ=255)

                                                                                                     acacTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATg                                                                           <  1:1003587/79‑1 (MQ=255)

                                                                                                        cTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTa                                                                                                 <  1:1224920/54‑1 (MQ=255)

                                                                                                        cTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTa                                                                                                 >  2:1224920/1‑54 (MQ=255)

                                                                                                        cTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAAt                                                                                        >  2:1013685/1‑63 (MQ=255)

                                                                                                        cTCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAAt                                                                                        <  1:1013685/63‑1 (MQ=255)

                                                                                                         tCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTaa                                                                                         <  2:1179558/61‑1 (MQ=255)

                                                                                                         tCGAAGAACAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTaa                                                                                         >  1:1179558/1‑61 (MQ=255)

                                                                                                             agaaCAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGca                                                        <  2:1453463/90‑1 (MQ=255)

                                                                                                             agaaCAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGca                                                        >  1:1453463/1‑90 (MQ=255)

                                                                                                                 cAGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACCAGCAGGAATCCCATCAGACGGGAGATCGCTTCAATGCCa   >  2:106301/1‑139 (MQ=255)

                                                                                                                  aGACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACCAGCAGGAATCCCATCAGACGGGAGATCGCTTCAATGCCAc  <  1:106301/139‑1 (MQ=255)

                                                                                                                   gACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACCAGCAGGaa                                  >  1:795309/1‑106 (MQ=255)

                                                                                                                   gACGCAATAATTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACCAGCAGGaa                                  <  2:795309/106‑1 (MQ=255)

TGAGTTTGCACTGGTCAATGTCGATGATTGGTTATGTGGGCGCGGTGCCTGCTTTTGCCGCGTTAATTTGGTCAATCATTATATTTCGCCGCTGGCCAGTGACACTCGAAGAACAGACGCAATAGTTGAAAGGCCCATTCGGGCCTTTTTTAATGGTACGTTTTAATGATTTCCAGGATGCCGTTAATAATAAACTGCACACCCATACATACCAGCAGGAATCCCATCAGACGGGAGATCGCTTCAATGCCAC  >  NC_000913/1618094‑1618346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A