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
A5 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,838,137	G→A	395 (TAG→TAA)	setC →	putative arabinose efflux transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,838,137	0	G	A	100.0%	149.8 / NA	48	395 (TAG→TAA)	setC	putative arabinose efflux transporter
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (22/26); total (22/26)

CGCGTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAGCTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAGGGG  >  NC_000913/3838003‑3838268

cgcgTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                 <  2:729013/139‑1 (MQ=255)

 gcgTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCAc                                                                                                                                <  2:320743/139‑1 (MQ=255)

                 cGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTc                                                                                                                           >  2:673165/1‑128 (MQ=255)

                 cGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTc                                                                                                                           <  1:673165/128‑1 (MQ=255)

                   ccGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGaaaa                                                                                                              <  2:549563/139‑1 (MQ=255)

                           gTTGACGGAATTGTGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCTCCAGTCTGGGCTAAGAAAAATCGGCGt                                                                                                      <  1:727856/139‑1 (MQ=255)

                               aCGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgcg                                                                                                  <  2:858921/139‑1 (MQ=255)

                                   aaTTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGt                                                                                                                            <  1:994552/109‑1 (MQ=255)

                                   aaTTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGt                                                                                                                            >  2:994552/1‑109 (MQ=255)

                                                             aTGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTa                                                                    >  2:966105/1‑139 (MQ=255)

                                                              tGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTAt                                                                   <  2:757640/139‑1 (MQ=255)

                                                                     ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              >  2:1115796/1‑105 (MQ=255)

                                                                     ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              <  1:1115796/105‑1 (MQ=255)

                                                                      tgtggctggcGATAGGGATGTGGGGTATTGAGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTg                                                           <  1:713607/137‑1 (MQ=255)

                                                                          gctggcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGcata                                                       >  2:825302/1‑139 (MQ=255)

                                                                           ctggcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCTATCCTCGCCATTTTTGCTATCa                                                                 >  1:1015536/1‑128 (MQ=255)

                                                                           ctggcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCa                                                                 <  2:1015536/128‑1 (MQ=255)

                                                                            tggcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGcataca                                                     <  1:32136/139‑1 (MQ=255)

                                                                             ggcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCAc                                                                                                                                <  2:1076066/63‑1 (MQ=255)

                                                                             ggcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGcatacat                                                    >  1:400499/1‑139 (MQ=255)

                                                                             ggcGATAGGGATGTTGGGGATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCAc                                                                                                                                >  1:1076066/1‑63 (MQ=255)

                                                                               cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              <  1:1026062/95‑1 (MQ=255)

                                                                               cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              >  2:1026062/1‑95 (MQ=255)

                                                                               cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTAt                                                                   >  2:250722/1‑122 (MQ=255)

                                                                               cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTAt                                                                   <  1:250722/122‑1 (MQ=255)

                                                                                     ggATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                            <  2:891524/139‑1 (MQ=255)

                                                                                     ggATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                            <  2:400499/139‑1 (MQ=255)

                                                                                                  tGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGc                                                                                                                      >  1:999970/1‑52 (MQ=255)

                                                                                                  tGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGc                                                                                                                      <  2:999970/52‑1 (MQ=255)

                                                                                                  tGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCag                               >  2:1184571/1‑139 (MQ=255)

                                                                                                    cGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCagag                             >  1:1112914/1‑139 (MQ=255)

                                                                                                        gatTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACagag                                                                                         <  1:901320/75‑1 (MQ=255)

                                                                                                        gatTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACagag                                                                                         >  2:901320/1‑75 (MQ=255)

                                                                                                        gatTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                            <  1:1144567/120‑1 (MQ=255)

                                                                                                        gatTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                            >  2:1144567/1‑120 (MQ=255)

                                                                                                         atTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGaaa                        >  2:704024/1‑139 (MQ=255)

                                                                                                                 gctgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGtt                >  2:117324/1‑139 (MQ=255)

                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCCGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                               <  1:647145/90‑1 (MQ=255)

                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCCGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                               >  2:647145/1‑90 (MQ=255)

                                                                                                                    gTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTcca             <  1:477815/139‑1 (MQ=255)

                                                                                                                     tttATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTccac            <  1:825302/139‑1 (MQ=255)

                                                                                                                               atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATaaa                                                 <  2:663977/92‑1 (MQ=255)

                                                                                                                               atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATaaa                                                 >  1:663977/1‑92 (MQ=255)

                                                                                                                               atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgggg  >  1:1134106/1‑139 (MQ=255)

                                                                                                                                 atTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgg    <  2:509255/135‑1 (MQ=255)

                                                                                                                                 atTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgg    >  1:509255/1‑135 (MQ=255)

                                                                                                                                  tttAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAttttt                                                                        >  1:20666/1‑66 (MQ=255)

                                                                                                                                  tttAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAttttt                                                                        <  2:20666/66‑1 (MQ=255)

CGCGTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAGCTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAGGGG  >  NC_000913/3838003‑3838268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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