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	2,225,978	G→A	45.9%	K139K (AAG→AAA)	dusB →	tRNA‑dihydrouridine synthase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,225,978	0	G	A	45.9%	8.4 / 48.1	61	K139K (AAG→AAA)	dusB	tRNA‑dihydrouridine synthase B
Reads supporting (aligned to +/- strand): ref base G (14/19); new base A (22/6); total (36/25)
Fisher's exact test for biased strand distribution p-value = 8.36e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.01e-01

AAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGAA  >  minE/2225925‑2226038

aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg                                                >  1:2661704/1‑68 (MQ=255)

aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg                                                >  1:1033450/1‑68 (MQ=255)

aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg                                                >  1:2421161/1‑68 (MQ=255)

aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg                                                >  1:790609/1‑68 (MQ=255)

aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATT‑‑CACCGGCTGGGc                                             >  1:1626182/1‑69 (MQ=255)

      aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc                                          >  1:2609043/1‑68 (MQ=255)

      aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc                                          >  1:2143936/1‑68 (MQ=255)

      aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc                                          >  1:3004765/1‑68 (MQ=255)

      aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc                                          >  1:2329604/1‑68 (MQ=255)

      aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc                                          >  1:2525067/1‑68 (MQ=255)

         cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa                                      <  1:947190/69‑1 (MQ=255)

         cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa                                      <  1:2014047/69‑1 (MQ=255)

         cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa                                      <  1:2328945/69‑1 (MQ=255)

         cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa                                      <  1:2710257/69‑1 (MQ=255)

         cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa                                      <  1:2822652/69‑1 (MQ=255)

         cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa                                      <  1:3189003/69‑1 (MQ=255)

               gAGGTCGTGAATTCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGt                                <  1:1769532/69‑1 (MQ=255)

               gAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGt                                <  1:1263782/69‑1 (MQ=255)

               gAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGt                                <  1:2158738/69‑1 (MQ=255)

                        aaTGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCg                         >  1:903014/1‑67 (MQ=255)

                           gCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAagag                    <  1:2668861/69‑1 (MQ=255)

                           gCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAagag                    <  1:2206666/69‑1 (MQ=255)

                           gCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAagag                    <  1:3323388/69‑1 (MQ=255)

                           gCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAagag                    <  1:1511223/69‑1 (MQ=255)

                           gCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAagag                    <  1:1463323/69‑1 (MQ=255)

                           gCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAagag                    <  1:984660/69‑1 (MQ=255)

                                 gACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTa                               >  1:2076187/1‑52 (MQ=255)

                                 gACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTa                               >  1:2054006/1‑52 (MQ=255)

                                 gACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTa                               >  1:353047/1‑52 (MQ=255)

                                   cGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCa            <  1:198105/69‑1 (MQ=255)

                                    gTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCaa           >  1:2015761/1‑69 (MQ=255)

                                    gTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCaa           >  1:2545063/1‑69 (MQ=255)

                                       ccTGTTACCTTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2849254/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACt         >  1:403106/1‑68 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2369522/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:649785/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2703435/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:974761/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2625563/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2468346/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2422673/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:1149743/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:1491769/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2191611/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2179207/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2109032/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2581243/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:2030592/1‑69 (MQ=255)

                                       ccTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTg        >  1:186263/1‑69 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGACCACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  >  1:2854273/1‑69 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:2100083/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:1121207/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  >  1:1321696/1‑69 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:1751070/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:437720/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:415879/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  >  1:1941036/1‑69 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:2198016/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:2720583/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:2262521/69‑1 (MQ=255)

                                             aCCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGaa  <  1:2578043/69‑1 (MQ=255)

AAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGCGAAGAGATTGCCCAACTGGCTGAA  >  minE/2225925‑2226038

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