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 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,860,110	G→A	71.7%	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	71.7%	76.1 / 40.3	53	V9I (GTC→ATC)	ygbJ	predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain
Reads supporting (aligned to +/- strand): ref base G (3/12); new base A (16/22); total (19/34)
Fisher's exact test for biased strand distribution p-value = 2.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

ATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTC  >  W3110S.gb/2860046‑2860173

atatCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCgg                                                             <  1:2674627/69‑1 (MQ=255)

   tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTAt                                                          <  1:216781/69‑1 (MQ=255)

   tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTAt                                                          <  1:1438138/69‑1 (MQ=255)

   tCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTAt                                                          <  1:1308281/69‑1 (MQ=255)

    caaacaaaATATCACTTAATTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                         >  1:3261217/1‑69 (MQ=255)

    caaacaaaATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTAt                                                          >  1:2007303/1‑68 (MQ=255)

    caaacaaaATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATc                                                         >  1:1014298/1‑69 (MQ=255)

         aaaaTATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTgg                                                    <  1:1476686/69‑1 (MQ=255)

         aaaaTATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTgg                                                    <  1:3234693/69‑1 (MQ=255)

         aaaaTATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTgg                                                    <  1:3679906/69‑1 (MQ=255)

            atatCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCtt                                                 <  1:3136618/69‑1 (MQ=255)

               tCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAgg                                              >  1:3064124/1‑69 (MQ=255)

               tCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAgg                                              >  1:979918/1‑69 (MQ=255)

               tCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAgg                                              >  1:2114317/1‑69 (MQ=255)

                   ttAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTc                                           <  1:2811605/68‑1 (MQ=255)

                   ttAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTc                                           <  1:1159137/68‑1 (MQ=255)

                     aaaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCtt                                                 <  1:393186/60‑1 (MQ=255)

                     aaaTTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCtt                                                 <  1:2328751/60‑1 (MQ=255)

                        ttAACTAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:1231158/69‑1 (MQ=255)

                        ttAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:2128797/69‑1 (MQ=255)

                        ttAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:1528433/69‑1 (MQ=255)

                        ttAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:2601448/69‑1 (MQ=255)

                        ttAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:997361/69‑1 (MQ=255)

                        ttAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:1962099/69‑1 (MQ=255)

                              aGGAGAGCAGATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgggaatggg                               <  1:2839341/69‑1 (MQ=255)

                                     ctgATGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagcagc                         <  1:2197001/66‑1 (MQ=255)

                                         tGAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGt                    <  1:2768642/69‑1 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCt                                                  >  1:2997320/1‑38 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCt                                                  >  1:1961090/1‑38 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTa                                                <  1:317535/40‑1 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTa                                                <  1:1259474/40‑1 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTa                                                <  1:1600936/40‑1 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTa                                                <  1:962269/40‑1 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTa                                                <  1:201045/40‑1 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTc                                           >  1:3519594/1‑45 (MQ=255)

                                          gAAAACGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGt                    >  1:3033205/1‑68 (MQ=255)

                                           aaaaCGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAg                                               >  1:3311824/1‑40 (MQ=255)

                                           aaaaCGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                                     >  1:3328200/1‑50 (MQ=255)

                                           aaaaCGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatgg                                      >  1:2374767/1‑49 (MQ=255)

                                           aaaaCGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                  <  1:1144012/69‑1 (MQ=255)

                                             aaCGTGATCTGAGTTTCATATCGGTATCGTTGGCTTa                                                <  1:2345842/37‑1 (MQ=37)

                                             aaCGGGCTCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                  >  1:320772/1‑67 (MQ=255)

                                             aaCGGGATCTGAGTTTCATATCGGTATCGTTGGCTTa                                                <  1:290432/37‑1 (MQ=255)

                                             aaCGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCata                >  1:1195317/1‑69 (MQ=255)

                                             aaCGGGATCTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                  >  1:2526466/1‑67 (MQ=255)

                                               cGGTATCTGAGTTTCATATCGTTATCGTTGGCTTa                                                <  1:1689433/35‑1 (MQ=25)

                                               cGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGagc                            >  1:2743757/1‑55 (MQ=255)

                                               cGGGATCTGAGTTTCATATCTGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGt                    <  1:2268797/63‑1 (MQ=255)

                                                     cTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:2861290/40‑1 (MQ=255)

                                                     cTGAGTTTCATATCGGTATCGTTGGCTTAGGGTCaatggg                                     <  1:994617/40‑1 (MQ=255)

                                                      tGAGTTTCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCa                  <  1:1764715/58‑1 (MQ=255)

                                                            tCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTc  >  1:3305533/1‑68 (MQ=255)

                                                            tCATATCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTc  >  1:1162920/1‑68 (MQ=255)

ATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTCGGTATCGTTGGCTTAGGGTCAATGGGAATGGGAGCAGCACTGTCATATGTCCGCGCAGGTC  >  W3110S.gb/2860046‑2860173

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