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	1,901,226	C→T	24.4%	T605T (ACG→ACA)	recB ←	exonuclease V (RecBCD complex), beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,901,226	0	C	T	24.4%	75.5 / 18.1	61	T605T (ACG→ACA)	recB	exonuclease V (RecBCD complex), beta subunit
Reads supporting (aligned to +/- strand): ref base C (26/20); new base T (7/8); total (33/28)
Fisher's exact test for biased strand distribution p-value = 5.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.08e-01

GCGCGTTCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAAC  >  minE/1901165‑1901282

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   <  1:487007/69‑1 (MQ=255)

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   <  1:2116892/69‑1 (MQ=255)

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   <  1:285945/69‑1 (MQ=255)

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   <  1:1965675/69‑1 (MQ=255)

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   <  1:3072191/69‑1 (MQ=255)

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   <  1:1562450/69‑1 (MQ=255)

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   <  1:2739752/69‑1 (MQ=255)

gcgcATTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACATTCGGGTGtcatca                                                   <  1:651576/69‑1 (MQ=255)

 cgcaTTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGtcatca                                                   >  1:2847672/1‑68 (MQ=255)

 cgcaTTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGTCATCAc                                                  >  1:932365/1‑69 (MQ=255)

 cgcaTTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGTCATCAc                                                  >  1:2146854/1‑69 (MQ=255)

 cgcaTTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGTCATCAc                                                  >  1:2513352/1‑69 (MQ=255)

 cgcaTTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGTCATCAc                                                  >  1:2815581/1‑69 (MQ=255)

 cgcaTTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGTCATCAc                                                  >  1:1557313/1‑69 (MQ=255)

 cgcaTTCAGCCCCATCATTGACGTTGCCAGCGCACTGCGCAGGGTGTTCTCACGTTCGGGTGTCATCAc                                                  >  1:1552229/1‑69 (MQ=255)

  gcgTTCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCAcc                                                 <  1:1155636/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:1779058/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:1863878/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:2027138/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:2869556/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:1276975/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:2483153/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:124085/69‑1 (MQ=255)

     ttCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGcc                                              <  1:3360472/69‑1 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:248281/1‑68 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:324432/1‑68 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:3065833/1‑68 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:2292200/1‑68 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:1590702/1‑68 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:4872/1‑68 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:2092940/1‑68 (MQ=255)

       cAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCt                                             >  1:2046358/1‑68 (MQ=255)

                 atTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCa                                   >  1:797897/1‑68 (MQ=255)

                      cGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCa                              <  1:2343696/68‑1 (MQ=255)

                      cGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCa                              <  1:760844/68‑1 (MQ=255)

                      cGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCa                              <  1:679651/68‑1 (MQ=255)

                          gCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTcc                         >  1:3077478/1‑69 (MQ=255)

                          gCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTcc                         >  1:3221103/1‑69 (MQ=255)

                          gCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTcc                         >  1:1672356/1‑69 (MQ=255)

                          gCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTcc                         >  1:1538342/1‑69 (MQ=255)

                          gCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTcc                         >  1:2169611/1‑69 (MQ=255)

                          gCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTcc                         >  1:365893/1‑69 (MQ=255)

                                gcACTACGCAGGGTGCTCTCACGTTCGGGCGTCATCACCGCCTGCAACACCCAAAGCATTTCCCGCGCt                   >  1:2143112/1‑69 (MQ=255)

                                gcACTACGCAGGGTGCTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTgcgc                    >  1:1115169/1‑68 (MQ=255)

                                gcACTACGCAGGGTGCTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCt                   >  1:1785831/1‑69 (MQ=255)

                                gcACTACGCAGGGTGCTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCt                   >  1:2705822/1‑69 (MQ=255)

                                gcACTACGCAGGGTGCTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACAAAAGCATTTCCTGCGCt                   >  1:2333187/1‑69 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:457684/69‑1 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:1042725/69‑1 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:2070216/69‑1 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:481187/69‑1 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:2366642/69‑1 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:2383787/69‑1 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:2406300/69‑1 (MQ=255)

                                        cAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGt           <  1:2669856/69‑1 (MQ=255)

                                                 ctcACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAac  >  1:23581/1‑69 (MQ=255)

                                                 ctcACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAac  >  1:2117045/1‑69 (MQ=255)

                                                 ctcACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAac  >  1:3132590/1‑69 (MQ=255)

                                                 ctcACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAac  >  1:3126498/1‑69 (MQ=255)

                                                 ctcACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAac  >  1:1517966/1‑69 (MQ=255)

                                                 ctcACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAac  >  1:1341634/1‑69 (MQ=255)

GCGCGTTCAGCCCCATCATTGACGTTGCCAGCGCACTACGCAGGGTGTTCTCACGTTCGGGCGTCATCACCGCCTGCAACAACCAAAGCATTTCCTGCGCTTCCAGAGTTTCAAAAAC  >  minE/1901165‑1901282

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