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 F28 I1 R2	164	48.3	4710601	85.3%	4018142	55.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	1,088,483	C→T	Q599Q (CAG→CAA)	ycdR ←	predicted enzyme associated with biofilm formation

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,088,483	0	C	T	100.0%	214.3 / NA	66	Q599Q (CAG→CAA)	ycdR	predicted enzyme associated with biofilm formation
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/46); total (20/46)

GCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCG  >  W3110S.gb/1088425‑1088535

gCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTg                                                    <  1:2233350/61‑1 (MQ=255)

gCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTg                                                    <  1:4166690/61‑1 (MQ=255)

gCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTg                                                    <  1:3985222/61‑1 (MQ=255)

      cATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATg                                             >  1:3560055/1‑62 (MQ=255)

      cATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATg                                             >  1:563798/1‑62 (MQ=255)

        tttttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtt                                           >  1:1357913/1‑62 (MQ=255)

        tttttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtt                                           >  1:8160/1‑62 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:3621933/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:4226490/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:411790/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:2681567/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:2691886/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:3680467/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:3176053/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:3601593/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:2902016/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:3113840/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:2215415/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:2146656/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:4525695/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:4634444/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:1518912/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:4708704/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:106593/62‑1 (MQ=255)

          tttCTGCCAGTTTTGTGCCGGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:1236549/62‑1 (MQ=255)

           ttCTGCGAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTGTTTAGCTTGAGGGATGtttt                                         <  1:3290251/61‑1 (MQ=255)

              tGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTaa                                      <  1:920812/61‑1 (MQ=255)

                ccAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAAt                                     >  1:2090951/1‑60 (MQ=255)

                ccAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAAt                                     >  1:4006025/1‑60 (MQ=255)

                ccAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAAt                                     >  1:1645764/1‑60 (MQ=255)

                ccAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAAt                                     >  1:46581/1‑60 (MQ=255)

                ccAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAAt                                     >  1:104628/1‑60 (MQ=255)

                     tttGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:4402213/51‑1 (MQ=255)

                             tGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTg                      <  1:3394598/62‑1 (MQ=255)

                             tGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTg                      <  1:3157468/62‑1 (MQ=255)

                             tGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTg                      <  1:2695346/62‑1 (MQ=255)

                             tGTAATTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTg                      <  1:249166/62‑1 (MQ=255)

                                aaTTCTAAAATAGATTTGTCTTTAGCTTGAGGGATGtttt                                         <  1:2275250/40‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATtttt                                          <  1:2574686/35‑1 (MQ=38)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:4229785/35‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:1498489/35‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:811251/35‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:2767292/35‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:650693/35‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:568377/35‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:2624736/35‑1 (MQ=255)

                                    cTAAAATAGATTTGTCTTTAGCTTGAGGGATGttt                                          <  1:1485480/35‑1 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTaa                                      >  1:3225065/1‑35 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTaa                                      >  1:2842122/1‑35 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTaa                                      >  1:1441915/1‑35 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCAtt           >  1:1484366/1‑62 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCAtt           >  1:1007825/1‑62 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCAtt           >  1:1782291/1‑62 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCAtt           >  1:4093162/1‑62 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCAtt           >  1:3760420/1‑62 (MQ=255)

                                        aaTAGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCAtt           >  1:297589/1‑62 (MQ=255)

                                           aGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTg          >  1:2577572/1‑60 (MQ=255)

                                           aGATTTGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTg          >  1:1047649/1‑60 (MQ=255)

                                               ttGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGc    <  1:4594878/62‑1 (MQ=255)

                                               ttGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGc    <  1:1884031/62‑1 (MQ=255)

                                               ttGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGc    <  1:2348858/62‑1 (MQ=255)

                                               ttGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGc    <  1:473577/62‑1 (MQ=255)

                                               ttGTCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGc    <  1:962677/62‑1 (MQ=255)

                                                  tCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCg  <  1:3981322/61‑1 (MQ=255)

                                                  tCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCg  <  1:282268/61‑1 (MQ=255)

                                                  tCTTTAGCTTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCg  <  1:8491/61‑1 (MQ=255)

GCTGACCATTTTTCTGCCAGTTTTGTGCCTGTAATTCTAAAATAGATTTGTCTTTAGCCTGAGGGATGTTTTTAATTTGATTGGTCAATTGTATTAACCATTGGTCAGCCG  >  W3110S.gb/1088425‑1088535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A