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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,945,691	G→A	57.8%	D873D (GAC→GAT)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,945,691	0	G	A	57.8%	16.5 / 47.5	64	D873D (GAC→GAT)	gcvP	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
Reads supporting (aligned to +/- strand): ref base G (12/15); new base A (27/10); total (39/25)
Fisher's exact test for biased strand distribution p-value = 3.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GACACCGGCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAT  >  minE/1945643‑1945744

gACACCTGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:5011/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGtt                                    >  1:89754/1‑68 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGtt                                    >  1:1345689/1‑68 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:395206/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:3286820/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:1462431/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:1921715/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:3111733/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:757890/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:3105197/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:910114/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:2622445/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:250619/1‑69 (MQ=255)

gACACCGGCTTTCACCTGATCAATTTCTGAGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:1843327/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGtt                                    >  1:1056712/1‑67 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:2662471/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:3293108/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:2342729/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:1793745/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:439607/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:1693625/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:615097/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:1383584/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:1254650/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:864680/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTcc                                  >  1:1081375/1‑69 (MQ=255)

 acacCGGCTTTCACCTGATCAATTTCTGCGCGGATAGCCAGCATCGCATCGATAAAGCGATCCAGTTc                                   >  1:1756200/1‑68 (MQ=255)

  cacCGGCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCGATCCAGTTCCa                                 >  1:1812163/1‑69 (MQ=255)

  cacCGGCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCGATCCAGTTCCa                                 >  1:2062885/1‑69 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:3141436/1‑45 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:936958/1‑45 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:2555979/1‑45 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:1062406/1‑45 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:1223287/1‑45 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:1317265/1‑45 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:18026/1‑45 (MQ=255)

      ggCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTc                                                     >  1:2072443/1‑45 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:2229838/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:1220393/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:512317/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:472666/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:1907504/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:3267113/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:192799/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:1943232/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:2116135/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:2615206/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:2479746/37‑1 (MQ=255)

                       tttCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:2528015/37‑1 (MQ=255)

                         tCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:2101780/35‑1 (MQ=255)

                         tCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCg                                            <  1:1908456/35‑1 (MQ=255)

                         tCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCGATCCAGTTCCACTTTGCTTTCAg                     <  1:1412772/58‑1 (MQ=255)

                         tCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCgg           >  1:252000/1‑68 (MQ=255)

                         tCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCgg           >  1:1195269/1‑68 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:2728371/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:1681291/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:2087464/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:1704801/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:3425845/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:2024635/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:905457/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:1196459/69‑1 (MQ=255)

                                 gATAGCCAGCATCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:1966060/69‑1 (MQ=255)

                                           aTCGCATCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAt  <  1:1925251/59‑1 (MQ=255)

GACACCGGCTTTCACCTGGTCAATTTCTGCGCGGATAGCCAGCATCGCGTCGATAAAGCGATCCAGTTCCACTTTGCTTTCAGATTCAGTCGGTTCAACCAT  >  minE/1945643‑1945744

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