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
A1 F28 I2 R2	356	55.1	4139924	95.4%	3949487	63.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,549,749	C→T	intergenic (+38/‑29)	fimC → / → fimD	chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,549,749	0	C	T	100.0%	197.7 / NA	63	intergenic (+38/‑29)	fimC/fimD	chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (34/29); total (34/29)

TACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACA  >  W3110S.gb/4549681‑4549814

tACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAattgattg                                                                 >  1:3606967/1‑71 (MQ=255)

tACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAattgattg                                                                 >  1:3039504/1‑71 (MQ=255)

tACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAattgattg                                                                 >  1:1509660/1‑71 (MQ=255)

             aCGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGAtttt                                                     >  1:3082423/1‑70 (MQ=255)

             aCGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGAtttt                                                     >  1:2881747/1‑70 (MQ=255)

             aCGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCAGAATAAAAAGAATTGATTGCCGGGTGAtttt                                                     >  1:1844545/1‑70 (MQ=255)

                      aTGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCggag                                            >  1:889396/1‑70 (MQ=255)

                         gAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaa                                         >  1:1844575/1‑70 (MQ=255)

                         gAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaa                                         >  1:248659/1‑70 (MQ=255)

                            tAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCgg                                              <  1:2040873/62‑1 (MQ=255)

                            tAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaataat                                     >  1:4138445/1‑71 (MQ=255)

                            tAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaataat                                     >  1:1516509/1‑71 (MQ=255)

                            tAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaataat                                     >  1:1797706/1‑71 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGAtt                                                       >  1:474565/1‑51 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaataa                                      >  1:1749289/1‑68 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   >  1:2543544/1‑71 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   >  1:3954985/1‑71 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   <  1:3471177/71‑1 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   <  1:960391/71‑1 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   <  1:1155717/71‑1 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   <  1:775411/71‑1 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   >  1:1581283/1‑71 (MQ=255)

                              aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGt                                   >  1:543433/1‑71 (MQ=255)

                                     gggAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaat                                        <  1:503172/59‑1 (MQ=255)

                                     gggAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATc                             >  1:2947550/1‑70 (MQ=255)

                                       gAATTTTTCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGaat                                        <  1:3502268/57‑1 (MQ=255)

                                          tttttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAtt                       >  1:2200650/1‑71 (MQ=255)

                                          tttttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAtt                       >  1:2970810/1‑71 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAtttt                      >  1:1633878/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:201557/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:1149217/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:3837450/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:2001263/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:2725622/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:2524670/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:1901346/1‑70 (MQ=255)

                                            tttCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt                      >  1:3608262/1‑70 (MQ=255)

                                              tCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTaa                    <  1:2845995/70‑1 (MQ=255)

                                              tCGCCTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTaa                    <  1:2059264/70‑1 (MQ=255)

                                                  cTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               <  1:3666374/71‑1 (MQ=255)

                                                  cTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               <  1:4040548/71‑1 (MQ=255)

                                                  cTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               <  1:3044321/71‑1 (MQ=255)

                                                  cTGAATAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               <  1:825165/71‑1 (MQ=255)

                                                     aaTATAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGAc                 <  1:3442001/66‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTTATATCTGAATTTAAGACttt              <  1:1978184/69‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGAc                 <  1:378281/66‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGAc                 <  1:2955457/66‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGAc                 <  1:2676982/66‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt              <  1:3522550/69‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt              <  1:1052864/69‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt              <  1:571105/69‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt              <  1:3866599/69‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt              <  1:3675434/69‑1 (MQ=255)

                                                     aaTAAAAAGAATTGATTGCCGGGGGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt              <  1:3019191/69‑1 (MQ=255)

                                                      aTAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACttt              <  1:3024113/68‑1 (MQ=255)

                                                       tAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               >  1:1020745/1‑66 (MQ=255)

                                                       tAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               >  1:491972/1‑66 (MQ=255)

                                                       tAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               >  1:149333/1‑66 (MQ=255)

                                                       tAAAAAGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACtt               >  1:1167702/1‑66 (MQ=255)

                                                         aaaaGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc        >  1:3169837/1‑71 (MQ=255)

                                                         aaaaGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc        >  1:746717/1‑71 (MQ=255)

                                                         aaaaGAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGc        >  1:1452476/1‑71 (MQ=255)

                                                             gAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGaaa    <  1:3921688/71‑1 (MQ=255)

                                                             gAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGaaa    <  1:2235275/71‑1 (MQ=255)

                                                             gAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGaaa    <  1:1783199/71‑1 (MQ=255)

                                                             gAATTGATTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGaaa    <  1:3595387/71‑1 (MQ=255)

                                                               attgattgCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAaca  <  1:141613/71‑1 (MQ=255)

TACCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACA  >  W3110S.gb/4549681‑4549814

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A