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 F21 I0 R2	308	27.9	1975068	96.7%	1909890	67.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,860,110	G→A	78.3%	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	78.3%	121.7 / 32.6	60	V9I (GTC→ATC)	ygbJ	predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain
Reads supporting (aligned to +/- strand): ref base G (5/8); new base A (24/23); total (29/31)
Fisher's exact test for biased strand distribution p-value = 5.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

TCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCT  >  W3110S.gb/2860049‑2860174

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCg                                                         >  1:974958/1‑71 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCg                                                         >  1:1935478/1‑71 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCg                                                         >  1:698189/1‑71 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCg                                                         >  1:1792035/1‑71 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCg                                                         >  1:1674962/1‑71 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:117528/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:419159/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:451328/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:208685/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:517354/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1959301/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:559125/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1712005/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:61074/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1607093/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1604838/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1415840/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1381411/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:823899/70‑1 (MQ=255)

tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1275163/70‑1 (MQ=255)

              aCTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTc                                            <  1:616373/70‑1 (MQ=255)

              aCTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTc                                            <  1:566302/70‑1 (MQ=255)

              aCTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTc                                            <  1:352912/70‑1 (MQ=255)

              aCTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTc                                            <  1:1796665/70‑1 (MQ=255)

              aCTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTc                                            <  1:722100/70‑1 (MQ=255)

               cTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                          <  1:1413604/55‑1 (MQ=255)

                         cAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTc                                            <  1:356506/59‑1 (MQ=255)

                                 gCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTTGGGTCAATGGGAATGGGAGCAGCAc                        <  1:1616812/71‑1 (MQ=255)

                                 gCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCAc                        <  1:1268913/71‑1 (MQ=255)

                                 gCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCAc                        <  1:912176/71‑1 (MQ=255)

                                     aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaat                                   <  1:130888/56‑1 (MQ=255)

                                     aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaat                                   <  1:262516/56‑1 (MQ=255)

                                     aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaat                                   <  1:1718547/56‑1 (MQ=255)

                                     aTGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaat                                   <  1:609797/56‑1 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTa                                                 >  1:244486/1‑40 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatgg                                 >  1:1973826/1‑56 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatgg                                 >  1:924460/1‑56 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatgg                                 >  1:527219/1‑56 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatgg                                 >  1:1233909/1‑56 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatgg                                 >  1:39385/1‑56 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatgg                                 >  1:1328556/1‑56 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                                      >  1:602504/1‑51 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTc                    >  1:1872484/1‑69 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:621371/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:996097/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:1225599/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:886593/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:856202/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:816067/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:1293228/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:63663/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:1563504/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:162163/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:1634529/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:1666301/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:527061/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:1036288/1‑70 (MQ=255)

                                       gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                   >  1:330601/1‑70 (MQ=255)

                                              ggATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTc                                            <  1:1264016/38‑1 (MQ=255)

                                                       tttCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCt  <  1:726336/71‑1 (MQ=255)

TCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTCT  >  W3110S.gb/2860049‑2860174

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