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	2,860,110	G→A	80.0%	V9I (GTC→ATC)	ygbJ →	predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,860,110	0	G	A	80.0%	115.8 / 26.0	55	V9I (GTC→ATC)	ygbJ	predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain
Reads supporting (aligned to +/- strand): ref base G (3/8); new base A (23/21); total (26/29)
Fisher's exact test for biased strand distribution p-value = 1.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

ACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCG  >  W3110S.gb/2860043‑2860167

acaATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATc                                                         <  1:1270180/70‑1 (MQ=255)

  aaTATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGt                                                      <  1:1557021/71‑1 (MQ=255)

   atatCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGt                                                      <  1:2690112/70‑1 (MQ=255)

   atatCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGt                                                      <  1:509683/70‑1 (MQ=255)

      tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:2725304/1‑71 (MQ=255)

      tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:224161/1‑71 (MQ=255)

      tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:2158408/1‑71 (MQ=255)

      tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:2810451/1‑71 (MQ=255)

      tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:2855965/1‑71 (MQ=255)

      tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:3282643/1‑71 (MQ=255)

      tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:896055/1‑71 (MQ=255)

      tCAAAAAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCg                                                  >  1:3235574/1‑71 (MQ=255)

           caaaATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTgg                                              >  1:796038/1‑70 (MQ=255)

           caaaATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTgg                                              >  1:1381292/1‑70 (MQ=255)

                    aCTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCTTTGGCTTAGGGTc                                     <  1:2781320/70‑1 (MQ=255)

                    aCTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTc                                     <  1:2991853/70‑1 (MQ=255)

                         aaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:2619434/71‑1 (MQ=255)

                         aaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:2614976/71‑1 (MQ=255)

                         aaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:115633/71‑1 (MQ=255)

                         aaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:680165/71‑1 (MQ=255)

                         aaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:352546/71‑1 (MQ=255)

                         aaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:1431785/71‑1 (MQ=255)

                         aaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgg                                <  1:3085663/70‑1 (MQ=255)

                                  ggAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagc                      <  1:1010364/71‑1 (MQ=255)

                                   gagtGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:919678/61‑1 (MQ=255)

                                    agagCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagcag                    <  1:2216634/71‑1 (MQ=255)

                                           aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatgg                          <  1:1855196/58‑1 (MQ=255)

                                           aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:3395278/53‑1 (MQ=255)

                                           aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:488166/53‑1 (MQ=255)

                                           aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:954286/53‑1 (MQ=255)

                                           aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                               <  1:2005843/53‑1 (MQ=255)

                                            tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGc                                             >  1:324936/1‑38 (MQ=255)

                                            tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaa                                   >  1:1534013/1‑48 (MQ=255)

                                            tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaa                                   >  1:2904784/1‑48 (MQ=255)

                                            tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaa                                   >  1:2007552/1‑48 (MQ=255)

                                            tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaa                                   >  1:3202827/1‑48 (MQ=255)

                                            tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaa                                   >  1:1736357/1‑48 (MQ=255)

                                            tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            <  1:1964824/71‑1 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            >  1:1978984/1‑70 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaa                             >  1:1770341/1‑53 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAgcagca                  >  1:506085/1‑64 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAgcagca                  >  1:194527/1‑64 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            >  1:1783554/1‑70 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            >  1:71014/1‑70 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            >  1:3448083/1‑70 (MQ=255)

                                             gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            >  1:1281367/1‑70 (MQ=255)

                                                      aTCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCcgcg  >  1:340640/1‑71 (MQ=255)

                                                      aTCTGAGTTTCATATCGGTATAGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCcgcg  >  1:2013048/1‑71 (MQ=255)

                                                       tCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            <  1:1074575/60‑1 (MQ=255)

                                                            gTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            <  1:3629885/55‑1 (MQ=255)

                                                            gTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            <  1:1898197/55‑1 (MQ=255)

                                                            gTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            <  1:2837502/55‑1 (MQ=255)

                                                            gTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa            <  1:2524758/55‑1 (MQ=255)

                                                             tttCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagcagc                   <  1:1847786/47‑1 (MQ=255)

                                                             tttCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagcagc                   <  1:2110095/47‑1 (MQ=255)

ACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCG  >  W3110S.gb/2860043‑2860167

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A