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 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,682,586	A→G	68.0%	Q439R (CAG→CGG)	ydgI →	predicted arginine/ornithine antiporter transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,682,586	0	A	G	68.0%	84.0 / 60.2	69	Q439R (CAG→CGG)	ydgI	predicted arginine/ornithine antiporter transporter
Reads supporting (aligned to +/- strand): ref base A (10/12); new base G (29/17); total (40/29)
Fisher's exact test for biased strand distribution p-value = 1.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.04e-01

CACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCT  >  W3110S.gb/1682520‑1682643

cACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCggg                                                         >  1:1285880/1‑69 (MQ=255)

cACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGa                                                        <  1:2074903/70‑1 (MQ=255)

cACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGa                                                        >  1:1441780/1‑70 (MQ=255)

cACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGa                                                        >  1:1752375/1‑70 (MQ=255)

cACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGa                                                        <  1:1974516/70‑1 (MQ=255)

cACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGa                                                        >  1:1195086/1‑70 (MQ=255)

cACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGa                                                        <  1:1077414/70‑1 (MQ=255)

  ccGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAAt                                                     >  1:738377/1‑71 (MQ=255)

        ctgctgGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCt                                               <  1:727135/71‑1 (MQ=255)

              gTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTgg                                         <  1:1969822/71‑1 (MQ=255)

              gTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTgg                                         <  1:144686/71‑1 (MQ=255)

                     tGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATg                                     <  1:2490390/68‑1 (MQ=255)

                     tGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATg                                     <  1:2025530/68‑1 (MQ=255)

                     tGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATg                                     <  1:514595/68‑1 (MQ=255)

                     tGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATg                                     <  1:332528/68‑1 (MQ=255)

                     tGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATg                                     <  1:336956/68‑1 (MQ=255)

                       tACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:750134/71‑1 (MQ=255)

                       tACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:1004638/71‑1 (MQ=255)

                       tACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:1396990/71‑1 (MQ=255)

                       tACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:1287507/71‑1 (MQ=255)

                       tACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:1206259/71‑1 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCTGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:1293824/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTgac                         >  1:84450/1‑63 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:2552663/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:1086384/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:3055994/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:1152732/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:805962/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:1733378/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGc                                        >  1:3546234/1‑50 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:3452296/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:2118318/1‑71 (MQ=255)

                                    cGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:3137307/1‑71 (MQ=255)

                                          cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCa                                       >  1:203081/1‑45 (MQ=255)

                                          cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCa                                       >  1:1394480/1‑45 (MQ=255)

                                          cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCa                                       >  1:2759235/1‑45 (MQ=255)

                                          cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGc              >  1:3156154/1‑70 (MQ=255)

                                          cccATGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGc              >  1:3726469/1‑70 (MQ=255)

                                              tGATAATGTACTGAACCGTCGGGAAATGGTGCTGa                                             <  1:3648947/35‑1 (MQ=255)

                                              tGATAATGTACTGAACCGTCGGGAAATGGTGCTGa                                             <  1:91179/35‑1 (MQ=255)

                                              tGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:1936588/48‑1 (MQ=255)

                                              tGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:1243792/48‑1 (MQ=255)

                                              tGATAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:2533042/48‑1 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTg                                  >  1:1664455/1‑44 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTg                                  >  1:1094781/1‑44 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTg                                  >  1:1099300/1‑44 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTg                                  >  1:636937/1‑44 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTg                                  >  1:1070931/1‑44 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTg                                  >  1:3189622/1‑44 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTaa                              >  1:212114/1‑48 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTg        >  1:1056586/1‑70 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTg        >  1:419146/1‑70 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTg        >  1:2820061/1‑70 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTg        >  1:2516151/1‑70 (MQ=255)

                                                aTAATGTACTGAACCGTCGGGAAATGGTGCTGATTGGCATCCTg                                  >  1:824207/1‑44 (MQ=37)

                                                aTAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGtt                   >  1:2223762/1‑59 (MQ=255)

                                                aTAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTg        >  1:102356/1‑70 (MQ=255)

                                                     gTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTc                  >  1:1102716/1‑55 (MQ=255)

                                                     gTACTGAACCGTCGGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCt  >  1:1674096/1‑71 (MQ=255)

                                                      tACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCt  <  1:2976957/70‑1 (MQ=255)

                                                        cTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:648523/38‑1 (MQ=255)

                                                        cTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:2810204/38‑1 (MQ=255)

                                                        cTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:206398/38‑1 (MQ=255)

                                                        cTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:1627960/38‑1 (MQ=255)

                                                        cTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:909649/38‑1 (MQ=255)

                                                          gAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTaa                              >  1:3629888/1‑38 (MQ=255)

                                                          gAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTaa                              >  1:3486551/1‑38 (MQ=255)

                                                          gAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTaa                              >  1:2420989/1‑38 (MQ=255)

                                                           aaCCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:3146574/35‑1 (MQ=255)

                                                           aaCCGTCGGGAAATGGTGCTGATTGGCATGCTGtt                                <  1:2932981/35‑1 (MQ=255)

CACCGGGGCTGCTGGTTTTCCTGTACGCGCGCAAAACGCATACCCATGATAATGTACTGAACCGTCAGGAAATGGTGCTGATTGGCATGCTGTTAATTGCCTCAGTTCCGGCGACCTGGATGCT  >  W3110S.gb/1682520‑1682643

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