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 I1 R2	328	63.0	4687567	98.0%	4593815	65.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,042,971	G→A	A39T (GCC→ACC)	livK →	leucine transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,042,971	0	G	A	100.0%	167.7 / NA	56	A39T (GCC→ACC)	livK	leucine transporter subunit
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/36); total (20/36)

CAATTTCACACACCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTGCCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACATTAATGCCAAAGGGGG  >  W3110S.gb/4042903‑4043038

cAATTTCACACACCGCTATGGCTGACGATATCAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTAcc                                                                    <  1:203908/71‑1 (MQ=255)

 aaTTTCACACACCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTAcc                                                                    >  1:3230951/1‑70 (MQ=255)

    ttCACACACCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGt                                                                >  1:4103775/1‑71 (MQ=255)

    ttCACACACCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGt                                                                >  1:332868/1‑71 (MQ=255)

    ttCACACACCGCTATGGCTGAAGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGt                                                                >  1:2578787/1‑71 (MQ=255)

     tCACACACCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑g                                                              >  1:1639838/1‑71 (MQ=255)

           acCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGa                                                        <  1:963746/71‑1 (MQ=255)

           acCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGa                                                        <  1:1349388/71‑1 (MQ=255)

              gCTATGGGTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGatat                                                     >  1:3132201/1‑71 (MQ=255)

              gCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGatat                                                     >  1:4636213/1‑71 (MQ=255)

              gCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGatat                                                     >  1:420192/1‑71 (MQ=255)

                  tGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATgg                                                   <  1:672278/69‑1 (MQ=255)

                     cTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAAttt                                              <  1:1165608/71‑1 (MQ=255)

                     cTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAAttt                                              <  1:3740231/71‑1 (MQ=255)

                     cTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAAttt                                              <  1:3250637/71‑1 (MQ=255)

                     cTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAAttt                                              <  1:2794201/71‑1 (MQ=255)

                        aCGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGa                                                        <  1:2985939/58‑1 (MQ=255)

                          gATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACgg                                         >  1:681991/1‑71 (MQ=255)

                              ttAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCa                                                                  >  1:484390/1‑43 (MQ=255)

                              ttAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCa                                                                  >  1:387904/1‑43 (MQ=255)

                              ttAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCa                                                                  >  1:4267753/1‑43 (MQ=255)

                              ttAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAAttt                                              <  1:2816265/62‑1 (MQ=255)

                              ttAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAAttt                                              <  1:2755764/62‑1 (MQ=255)

                                aaaGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGgcgcgc                                    >  1:589047/1‑70 (MQ=255)

                                aaaGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGcgcgcg                                   >  1:3926589/1‑71 (MQ=255)

                                    tCGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGTGGGGGCGATATGGAATTTAACGGCGCGCGTCa                                <  1:1511785/71‑1 (MQ=255)

                                     cGCCGTTGTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGa                                                        <  1:1202791/45‑1 (MQ=255)

                                            gTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGata                                                      >  1:3299360/1‑40 (MQ=255)

                                            gTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTa                        <  1:3458962/70‑1 (MQ=255)

                                            gTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTa                        <  1:842843/70‑1 (MQ=255)

                                            gTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTa                        <  1:65385/70‑1 (MQ=255)

                                            gTCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTa                        <  1:4601905/70‑1 (MQ=255)

                                             tCGGCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTaaa                      <  1:3635904/71‑1 (MQ=255)

                                               ggCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTaa                                            >  1:3905366/1‑47 (MQ=255)

                                               ggCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGa                    <  1:3915564/71‑1 (MQ=255)

                                               ggCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGa                    <  1:3800433/71‑1 (MQ=255)

                                               ggCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGa                    <  1:946424/71‑1 (MQ=255)

                                               ggCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGa                    >  1:3273538/1‑71 (MQ=255)

                                               ggCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGa                    <  1:1385935/71‑1 (MQ=255)

                                               ggCGCGATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGa                    <  1:3099448/71‑1 (MQ=255)

                                                  gcgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGAc                   >  1:4267065/1‑69 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:2295641/71‑1 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:4177642/71‑1 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:450631/71‑1 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:4660280/71‑1 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:4668983/71‑1 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:2938254/71‑1 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGACAATTAAAGACAtt                <  1:2795700/71‑1 (MQ=255)

                                                   cgATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGCAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:3410666/71‑1 (MQ=255)

                                                    gATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:1120463/70‑1 (MQ=255)

                                                    gATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:4346151/70‑1 (MQ=255)

                                                    gATGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACAtt                <  1:4282597/70‑1 (MQ=255)

                                                     aTGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACATTaa              >  1:4080478/1‑71 (MQ=255)

                                                     aTGTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACATTaa              <  1:3645003/71‑1 (MQ=255)

                                                       gTCCGGCCCGATTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACATTAATg            >  1:3278404/1‑71 (MQ=255)

                                                                 aTTACCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACATTAATGCCAAAggggg  <  1:3357704/71‑1 (MQ=255)

CAATTTCACACACCGCTATGGCTGACGATATTAAAGTCGCCGTTGTCGGCGCGATGTCCGGCCCGATTGCCCAGT‑GGGGCGATATGGAATTTAACGGCGCGCGTCAGGCAATTAAAGACATTAATGCCAAAGGGGG  >  W3110S.gb/4042903‑4043038

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