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 F8 I0 R1	311	50.1	4085234	95.9%	3917739	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,093,680	G→A	23.2%	H19H (CAC→CAT)	yggR ←	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,093,680	0	G	A	23.2%	111.1 / 30.5	56	H19H (CAC→CAT)	yggR	predicted transporter
Reads supporting (aligned to +/- strand): ref base G (20/23); new base A (7/6); total (27/29)
Fisher's exact test for biased strand distribution p-value = 7.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

GCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATCCTCG  >  W3110S.gb/3093613‑3093749

gCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGatg                                                                     >  1:3966305/1‑70 (MQ=255)

 cGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGgtg                                                                     >  1:1364564/1‑69 (MQ=255)

       aaaCGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATcc                                                              >  1:965476/1‑70 (MQ=255)

       aaaCGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATcc                                                              >  1:3925524/1‑70 (MQ=255)

           ggCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGAc                                                         <  1:1227698/71‑1 (MQ=255)

              gcAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGt                                                       >  1:275783/1‑70 (MQ=255)

               cAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTa                                                     <  1:2298683/71‑1 (MQ=255)

                  cTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGAc                                                         >  1:3775223/1‑64 (MQ=255)

                  cTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGc                                                  >  1:1838548/1‑71 (MQ=255)

                     ccATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCtt                                                <  1:3758980/70‑1 (MQ=255)

                      cATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTa                                              <  1:1285972/71‑1 (MQ=255)

                        ttCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGATGTa                                                                   <  1:3362186/48‑1 (MQ=255)

                         tCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTaca                                            >  1:1047673/1‑70 (MQ=255)

                          cTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCg                                                             >  1:240521/1‑52 (MQ=255)

                          cTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTacac                                           >  1:842960/1‑70 (MQ=255)

                          cTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTacac                                           >  1:941934/1‑70 (MQ=255)

                          cTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTacac                                           >  1:496531/1‑70 (MQ=255)

                             ccGCGAATGCGCCATCGTGCGGGCCAGTCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTa                                         <  1:2718303/69‑1 (MQ=255)

                             ccGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTaa                                        <  1:2221154/70‑1 (MQ=255)

                             ccGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTa                                         <  1:1553776/69‑1 (MQ=255)

                             ccGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGTTATGCTTTACACTa                                         <  1:1189812/69‑1 (MQ=255)

                                  aaTGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACt                                          <  1:3664371/63‑1 (MQ=255)

                                  aaTGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACt                                          <  1:3412712/63‑1 (MQ=255)

                                       gcCATCGTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGTTATGCTTTACACTAGGGGCCACAAtt                             <  1:2552110/71‑1 (MQ=255)

                                          aTCGTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGTTATGCtt                                                >  1:1965003/1‑49 (MQ=255)

                                           tCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCtt                                                <  1:2550902/48‑1 (MQ=255)

                                           tCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCcaca                                <  1:515728/64‑1 (MQ=255)

                                            cGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCgaga                                                          >  1:3937113/1‑37 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTaca                                            >  1:1617514/1‑50 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTa                                              >  1:1474771/1‑48 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATttcttc                        >  1:1116181/1‑70 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATttcttc                        <  1:919765/70‑1 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATttcttc                        >  1:3266589/1‑70 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATttcttc                        <  1:3069419/70‑1 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGTTATGCTTTaca                                            >  1:118672/1‑50 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGTTATGCTTTaca                                            >  1:123320/1‑50 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGTTATGCTTTaca                                            >  1:2953695/1‑50 (MQ=255)

                                             gTGCGGGCCAGGCGCTGCACAGATGTAGATCCGAGACGTTATGCTTTaca                                            >  1:1620731/1‑50 (MQ=255)

                                              tGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATttcttc                        <  1:331953/69‑1 (MQ=255)

                                                    ccAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCa                <  1:1772783/71‑1 (MQ=255)

                                                    ccAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCa                <  1:412553/71‑1 (MQ=255)

                                                    ccAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACAAAGGGCCACAATTTCTTCCATATTCa                <  1:2965210/71‑1 (MQ=255)

                                                     cAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTa                                         <  1:249112/45‑1 (MQ=255)

                                                     cAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTa                                         <  1:3521975/45‑1 (MQ=255)

                                                     cAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTa                                         <  1:271433/45‑1 (MQ=255)

                                                     cAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCa                >  1:2721625/1‑70 (MQ=255)

                                                     cAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCa                >  1:3809154/1‑70 (MQ=255)

                                                     cAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCa                >  1:3345059/1‑70 (MQ=255)

                                                     cAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCa                >  1:3114483/1‑70 (MQ=255)

                                                       ggCGCTGCACAGATGTAGATCCGAGACGTTATGCTTTa                                              <  1:1479659/38‑1 (MQ=255)

                                                        gcgcTGCACAGGTGTAGATCCGAGACTTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCa                <  1:3204620/67‑1 (MQ=255)

                                                        gcgcTGCACAGGTGTAGATCCGAGACGTTATGCTTTa                                              <  1:3752290/37‑1 (MQ=255)

                                                        gcgcTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACt            <  1:4063448/71‑1 (MQ=255)

                                                         cgcTGCACAGATGTAGATCCGAGACGTTATGCTTTaca                                            >  1:2833430/1‑38 (MQ=255)

                                                              cacaGATGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCAt               <  1:3531741/62‑1 (MQ=255)

                                                              cacaGATGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCAt               <  1:4004982/62‑1 (MQ=255)

                                                                 aGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATCCTc   >  1:3474315/1‑71 (MQ=255)

                                                                 aGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATCCTc   >  1:2906188/1‑71 (MQ=255)

                                                                  ggTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATCCTCg  >  1:1877060/1‑71 (MQ=255)

                                                                   gtgtAGATCCGAGACGTTATGCTTTACACTAAGGGCcaca                                <  1:2512214/40‑1 (MQ=255)

                                                                   gtgtAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATCCTCg  >  1:2828312/1‑70 (MQ=255)

                                                                   gtgtAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATCCTCg  >  1:1465862/1‑70 (MQ=255)

                                                                   gtgtAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATACTCg  >  1:3638455/1‑70 (MQ=255)

GCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAGATCCGAGACGTTATGCTTTACACTAAGGGCCACAATTTCTTCCATATTCATACTAAGATCCTCG  >  W3110S.gb/3093613‑3093749

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A