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 I2 R1	58	36.1	1832140	90.7%	1661750	105.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,984,271	A→G	intergenic (‑147/+140)	kduI ← / ← yqeF	hexuronate isomerase/short chain acyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,271	0	A	G	100.0%	121.8 / NA	33	intergenic (‑147/+140)	kduI/yqeF	hexuronate isomerase/short chain acyltransferase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/16); total (17/16)

GATAATCAGTGAAGCGTGAAAATAGAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAAAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGC  >  NC_000913/2984135‑2984406

gATAATCAGTGAAGCGTGAAAATAGAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTaagaa                                                                                                                                       <  2:575145/139‑1 (MQ=255)

       aGTGAAGCGTGAAAATAGAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCa                                                                                                                                <  1:689751/139‑1 (MQ=255)

          gAAGCGTGAAAATAGAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAgtg                                                                                                                             <  2:205782/139‑1 (MQ=255)

               gTGAAAATAGAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGAt                                                                                                                        <  1:665916/139‑1 (MQ=255)

                tGAAAATAGAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGATAAGGATTAAGAAAAGTGCAGTGTCGATc                                                                                                                       >  2:506095/1‑139 (MQ=255)

                        gAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAatat                                                                                                               <  1:863038/139‑1 (MQ=255)

                                                  ttttCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAg                                                                                     <  2:599544/139‑1 (MQ=255)

                                                                   tgatATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGaa                                                                                                                  <  2:861029/93‑1 (MQ=255)

                                                                   tgatATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGaa                                                                                                                  >  1:861029/1‑93 (MQ=255)

                                                                     atatGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTg                                                                                                                                  <  1:639785/75‑1 (MQ=255)

                                                                     atatGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTg                                                                                                                                  >  2:639785/1‑75 (MQ=255)

                                                                         gCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTg                                                              >  1:108841/1‑139 (MQ=255)

                                                                                     gggTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGcc                                                                                   <  1:405172/106‑1 (MQ=255)

                                                                                     gggTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGcc                                                                                   >  2:405172/1‑106 (MQ=255)

                                                                                         tttCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTgccagc                                                         >  2:591647/1‑128 (MQ=255)

                                                                                         tttCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTgccagc                                                         <  1:591647/128‑1 (MQ=255)

                                                                                           tCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTaagaa                                                                                                                                       >  1:512568/1‑48 (MQ=255)

                                                                                           tCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTaagaa                                                                                                                                       <  2:512568/48‑1 (MQ=255)

                                                                                                tAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAg                                                                                >  1:48543/1‑98 (MQ=255)

                                                                                                tAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAg                                                                                <  2:48543/98‑1 (MQ=255)

                                                                                                  aaaaTAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTgccagc                                                         <  2:841534/119‑1 (MQ=255)

                                                                                                  aaaaTAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTgccagc                                                         >  1:841534/1‑119 (MQ=255)

                                                                                                  aaaaTAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCcat                                                      >  1:508351/1‑122 (MQ=255)

                                                                                                  aaaaTAAAACAATGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCcat                                                      <  2:508351/122‑1 (MQ=255)

                                                                                                              tGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCAt                                                                                                          >  2:669577/1‑58 (MQ=255)

                                                                                                              tGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCAt                                                                                                          <  1:669577/58‑1 (MQ=255)

                                                                                                              tGTTTCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATTTAGGAGAACTGGCAGGCCTCAATTATTCAACA‑ATTaaataagggaaaaa                        >  2:130512/1‑127 (MQ=255)

                                                                                                                tttCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGatat                       >  2:60701/1‑139 (MQ=255)

                                                                                                                tttCATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGatat                       >  2:790866/1‑139 (MQ=255)

                                                                                                                   cATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGc                                                                                    >  2:61757/1‑75 (MQ=255)

                                                                                                                   cATTTTTAAGTTAAGGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGc                                                                                    <  1:61757/75‑1 (MQ=255)

                                                                                                                              taagGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCcat                                                      >  1:851689/1‑94 (MQ=255)

                                                                                                                              taagGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCcat                                                      <  2:851689/94‑1 (MQ=255)

                                                                                                                                agGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACgg                              <  2:323954/116‑1 (MQ=255)

                                                                                                                                agGATTAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACgg                              >  1:323954/1‑116 (MQ=255)

                                                                                                                                     tAAGAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGc  >  2:704318/1‑139 (MQ=255)

GATAATCAGTGAAGCGTGAAAATAGAAAACGATAGTGAAACACTGTTTCGTTTTCTCTATAAAGGGATGATATGCCCATGGGCTAGGGTTTTCAATTAAAAATAAAACAATGTTTCATTTTTAAGTTAAGGATTAAAAAAAGTGCAGTGTCGATCACGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGC  >  NC_000913/2984135‑2984406

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A