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	443,240	G→A	26.1%	G174G (GGC→GGT)	speF ←	ornithine decarboxylase isozyme, inducible

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	443,240	0	G	A	26.1%	66.2 / 18.3	57	G174G (GGC→GGT)	speF	ornithine decarboxylase isozyme, inducible
Reads supporting (aligned to +/- strand): ref base G (16/26); new base A (7/8); total (23/34)
Fisher's exact test for biased strand distribution p-value = 7.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACGAAGTAGGTTTTATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGCC  >  minE/443177‑443306

aaCGAAGTAGGTTTTATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCtt                                                                <  1:2252819/68‑1 (MQ=255)

aaCGAAGTAGGTTTTATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCtt                                                                <  1:2019666/68‑1 (MQ=255)

aaCGAAGTAGGTTTTATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCtt                                                                <  1:937563/68‑1 (MQ=255)

aaCGAAGTAGGTTTTATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCtt                                                                <  1:3200825/68‑1 (MQ=255)

 aCGAAGTAGGTTTTATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCtt                                                                <  1:2870704/67‑1 (MQ=255)

           ttttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagca                                                    <  1:993111/69‑1 (MQ=255)

           ttttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagca                                                    <  1:2003341/69‑1 (MQ=255)

           ttttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagca                                                    <  1:3270332/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGTATcagcag                                                   <  1:2117492/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagcag                                                   <  1:1373015/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagcag                                                   <  1:629468/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagcag                                                   <  1:3093638/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagcag                                                   <  1:2895602/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagcag                                                   <  1:112846/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagcag                                                   <  1:2691573/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagcag                                                   <  1:1027132/69‑1 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATcagca                                                    >  1:221263/1‑68 (MQ=255)

            tttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATc                                                        >  1:2345477/1‑64 (MQ=255)

             ttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATc                                                        >  1:1429592/1‑63 (MQ=255)

             ttATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATc                                                        >  1:2794263/1‑63 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:951395/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:732949/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:3036427/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:3334457/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:2589691/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:1468049/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:1188877/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGAAGATCGcc                                             <  1:1335858/69‑1 (MQ=255)

                  ggCATTAAACACTTTTGCCGCATGTAGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGcc                                             <  1:844562/69‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:1458228/68‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:1461687/68‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:2981123/68‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:1765438/68‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:1841596/68‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:2229102/68‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:2517627/68‑1 (MQ=255)

                    cATTAAACACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCAccc                                            <  1:2089219/68‑1 (MQ=255)

                        aaaCACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGc                                       >  1:2932650/1‑69 (MQ=255)

                        aaaCACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGc                                       >  1:1457489/1‑69 (MQ=255)

                        aaaCACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGc                                       >  1:360799/1‑69 (MQ=255)

                        aaaCACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGc                                       >  1:787286/1‑69 (MQ=255)

                         aaCACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATcagaa                                                    >  1:1982993/1‑53 (MQ=255)

                         aaCACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCACCCATTGca                                      >  1:1318859/1‑68 (MQ=255)

                         aaCACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCACCCATTGca                                      >  1:3301183/1‑68 (MQ=255)

                         aaCACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCACCCATTGca                                      >  1:352689/1‑68 (MQ=255)

                         aaCACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCACCCATTGca                                      >  1:1189236/1‑68 (MQ=255)

                         aaCACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCACCCATTGca                                      >  1:2602378/1‑68 (MQ=255)

                         aaCACTTTAGCCGCATGTTGCTGTGCAATGCATGGCGCACCTTCATGAATCAGAAGATCACCCATTGca                                      >  1:2524431/1‑68 (MQ=255)

                           cacTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTAc                                    <  1:2519555/69‑1 (MQ=255)

                             cTTTTGCCGCATGTTGCTGTGCAATGCATGTCGCGCCTTCGTGAATc                                                        >  1:1257114/1‑47 (MQ=255)

                             cTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGt                                  >  1:2940839/1‑69 (MQ=255)

                             cTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGt                                  >  1:2286845/1‑69 (MQ=255)

                                                          ggCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAgc     >  1:1107246/1‑69 (MQ=255)

                                                          ggCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAgc     >  1:3417022/1‑69 (MQ=255)

                                                          ggCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAgc     >  1:317494/1‑69 (MQ=255)

                                                          ggCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAgc     >  1:3161415/1‑69 (MQ=255)

                                                          ggCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAgc     >  1:2963793/1‑69 (MQ=255)

                                                             gcgcCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGcc  <  1:361372/69‑1 (MQ=255)

                                                             gcgcCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGcc  <  1:581962/69‑1 (MQ=255)

                                                             gcgcCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGcc  <  1:3301474/69‑1 (MQ=255)

                                                             gcgcCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGcc  <  1:916189/69‑1 (MQ=255)

                                                             gcgcCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGcc  <  1:1830118/69‑1 (MQ=255)

                                                             gcgcCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGcc  <  1:1852498/69‑1 (MQ=255)

AACGAAGTAGGTTTTATCGGCATTAAACACTTTTGCCGCATGTTGCTGTGCAATGCATGGCGCGCCTTCGTGAATCAGCAGATCGCCCATCGCTACGTCGGCGTTGCACAAGTCGGCACGGAACAGCGCC  >  minE/443177‑443306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A