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	2,005,368	T→C	23.9%	T128A (ACC→GCC)	hybC ←	hydrogenase 2, large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,005,368	0	T	C	23.9%	59.3 / 14.3	50	T128A (ACC→GCC)	hybC	hydrogenase 2, large subunit
Reads supporting (aligned to +/- strand): ref base T (28/10); new base C (5/7); total (33/17)
Fisher's exact test for biased strand distribution p-value = 7.74e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.46e-01

CTCTTCCGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAGAAATGAACA  >  minE/2005309‑2005435

ctctTCCGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGc                                                            >  1:814497/1‑69 (MQ=255)

ctctTCCGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGc                                                            >  1:2979072/1‑69 (MQ=255)

ctctTCCGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGc                                                            >  1:1789895/1‑69 (MQ=255)

ctctTCCGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGc                                                            >  1:1687183/1‑69 (MQ=255)

     ccGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTtg                                                         <  1:127882/67‑1 (MQ=255)

     ccGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTtg                                                         <  1:1291330/67‑1 (MQ=255)

     ccGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTtg                                                         <  1:2475908/67‑1 (MQ=255)

     ccGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTtg                                                         <  1:1681147/67‑1 (MQ=255)

       ggACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTtgcag                                                      <  1:902226/68‑1 (MQ=255)

       ggACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTtgcag                                                      <  1:2353883/68‑1 (MQ=255)

       ggACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTtgcag                                                      <  1:2197542/68‑1 (MQ=255)

               cAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGt                                             <  1:2008872/69‑1 (MQ=255)

               cAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGt                                             >  1:2043792/1‑69 (MQ=255)

               cAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGt                                             >  1:2976230/1‑69 (MQ=255)

                           cGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCa                                 >  1:630991/1‑69 (MQ=255)

                           cGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCa                                 >  1:2067132/1‑69 (MQ=255)

                           cGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCa                                 >  1:2877523/1‑69 (MQ=255)

                            gAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAg                                >  1:1475543/1‑69 (MQ=255)

                               aCGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTcc                             <  1:2012595/69‑1 (MQ=255)

                               aCGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTcc                             <  1:2690499/69‑1 (MQ=255)

                                     ttCAGCATTTCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAgcgc                        >  1:2952797/1‑68 (MQ=255)

                                     ttCAGCATTTCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAgcgc                        >  1:1608064/1‑68 (MQ=255)

                                     ttCAGCATTTCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAgcgc                        >  1:1501133/1‑68 (MQ=255)

                                     ttCAGCATTTCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAgcgc                        >  1:2864141/1‑68 (MQ=255)

                                     ttCAGCATTTCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAgcgc                        >  1:2833470/1‑68 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCAGCCAGTCCAGCGCCGAAAGCt                >  1:1624558/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:3263695/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:3292697/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:528806/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:68406/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:818424/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:230904/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:1613376/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:2650934/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:1680264/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:1775977/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:2289585/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:1803556/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCt                >  1:1830762/1‑67 (MQ=255)

                                              tCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGa              <  1:1251638/69‑1 (MQ=255)

                                              tCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGa              <  1:489101/69‑1 (MQ=255)

                                              tCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGa              <  1:3332375/69‑1 (MQ=255)

                                              tCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGa              <  1:1209337/69‑1 (MQ=255)

                                              tCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGa              <  1:252946/69‑1 (MQ=255)

                                              tCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGa              <  1:2839916/69‑1 (MQ=255)

                                              tCGGAGGCTTTGGCTGGATCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGa              <  1:2781276/69‑1 (MQ=255)

                                                   ggCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCa                            >  1:2977872/1‑50 (MQ=255)

                                                   ggCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAg           >  1:1462324/1‑67 (MQ=255)

                                                   ggCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAGaa         >  1:535679/1‑69 (MQ=255)

                                                   ggCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAGa          >  1:2692075/1‑68 (MQ=255)

                                                           ttggGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAGAAATGAACa  <  1:1841260/68‑1 (MQ=255)

                                                           ttggGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAGAAATGAACa  <  1:213809/68‑1 (MQ=255)

                                                           ttggGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAGAAATGAACa  <  1:1353571/68‑1 (MQ=255)

CTCTTCCGGACTGTTCAGGTGCCAGGTCGAAACGCCTTTCAGCATTTCGGAGGCTTTGGTTGGGTCAGCTTGCAGTGCAGAAGTGATGTCCACCCAGTCCAGCGCCGAAAGCTGATAGAAATGAACA  >  minE/2005309‑2005435

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A