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 F3 I0 R1	560	56.4	4650532	94.9%	4413354	59.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	556,858	A→T	100%	L36Q (CTG→CAG)	folD ←	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	556,858	0	A	T	100.0%	94.7 / NA	34	L36Q (CTG→CAG)	folD	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (14/20); total (14/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CACAAGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCAGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACTTCAGAGCGCACCTG  >  W3110S.gb/556790‑556925

cacaAGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGt                                                                   >  1:2524759/1‑71 (MQ=255)

  caAGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTcc                                                                 <  1:1544366/71‑1 (MQ=255)

  caAGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTcc                                                                 <  1:1762196/71‑1 (MQ=255)

   aaGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCt                                                                <  1:4337329/71‑1 (MQ=255)

   aaGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCt                                                                <  1:1871420/71‑1 (MQ=255)

   aaGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCt                                                                <  1:2172019/71‑1 (MQ=255)

     gCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTgg                                                              >  1:3751814/1‑71 (MQ=255)

          gCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGccc                                                         >  1:2816419/1‑71 (MQ=255)

           cGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCg                                                        <  1:565459/71‑1 (MQ=255)

           cGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGACCTGGTGCCCg                                                        >  1:749405/1‑71 (MQ=255)

             tttGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCa                                                      <  1:1316527/71‑1 (MQ=255)

             tttGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCa                                                      <  1:4437892/71‑1 (MQ=255)

               tgcttgcGACATAAATTTGCGATGCAGGGTTTCTACCCACCAGCACAACGGCCTGTCCTgg                                                              >  1:365078/1‑61 (MQ=255)

                  ttgcGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTcc                                                                 <  1:359271/55‑1 (MQ=255)

                       aCATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGc                                            <  1:4633227/71‑1 (MQ=255)

                       aCATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGc                                            <  1:3290864/71‑1 (MQ=255)

                         aTAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCaa                                          <  1:3663244/71‑1 (MQ=255)

                          tAAATTTGCGATGCAGGGTTACTACCCAACAGCACAACGGCCTGTcc                                                                 <  1:4380098/47‑1 (MQ=255)

                           aaaTTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGt                                                                   >  1:199932/1‑44 (MQ=255)

                            aaTTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATa                                        >  1:2138298/1‑70 (MQ=255)

                            aaTTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATAc                                       >  1:28117/1‑71 (MQ=255)

                                   gATGCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTg                                <  1:2090516/71‑1 (MQ=255)

                                      gCAGGGTTACTACCCACCAGCACAACGGCCTGTCCTg                                                               >  1:2303037/1‑37 (MQ=255)

                                              actacCCACCAGCACAACTGCCTGTCCTGGTGCCCGCAGTCCgt                                                >  1:3319778/1‑43 (MQ=38)

                                                  cccACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGc                    <  1:1559724/68‑1 (MQ=255)

                                                  cccACCAGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAAc                 >  1:1547065/1‑71 (MQ=255)

                                                    caccaGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACtt               <  1:389901/71‑1 (MQ=255)

                                                    caccaGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACtt               <  1:2169204/71‑1 (MQ=255)

                                                      ccaGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACtt               >  1:2240168/1‑69 (MQ=255)

                                                       caGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACTTCag            <  1:4311872/71‑1 (MQ=255)

                                                        aGCACAACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACTTCa             >  1:4571973/1‑69 (MQ=255)

                                                            caACGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACTTCAGAgcgc       <  1:3416133/71‑1 (MQ=255)

                                                              aCGGCCTGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAg                     >  1:4425022/1‑55 (MQ=255)

                                                                 gCCTGTACTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACTTCAGAGCGCACctg  <  1:1909605/71‑1 (MQ=255)

CACAAGCCTTGCGTTTGCTTGCGACATAAATTTGCGATGCAGGGTTACTACCCACCAGCACAACGGCCAGTCCTGGTGCCCGCAGTCCGGCTGCAATACGCGCCTGAACTTTTTGAGCAACTTCAGAGCGCACCTG  >  W3110S.gb/556790‑556925

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