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	2,640,148	T→G	24.3%	I33I (ATA→ATC)	yhhA ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,640,148	0	T	G	24.3%	99.7 / 37.1	74	I33I (ATA→ATC)	yhhA	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (18/38); new base G (2/16); total (20/54)
Fisher's exact test for biased strand distribution p-value = 1.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.91e-01

GATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGC  >  minE/2640081‑2640214

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGTCTGGGTa                                                                   <  1:2587048/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:1957502/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:554418/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:2845343/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:304885/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:3398275/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:3218226/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:3135859/69‑1 (MQ=255)

gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGGCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa                                                                   <  1:526671/69‑1 (MQ=255)

    cAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCt                                                                >  1:611344/1‑68 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:1569732/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:3191934/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:3112868/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:391274/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:2934609/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:421790/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:2836901/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:577602/68‑1 (MQ=255)

      gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:2209446/68‑1 (MQ=255)

       cATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa                                                              <  1:996541/67‑1 (MQ=255)

        aTCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATat                                                           >  1:469069/1‑68 (MQ=255)

        aTCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATat                                                           >  1:3111371/1‑68 (MQ=255)

           ccTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATAcccc                                                        >  1:1925114/1‑69 (MQ=255)

           ccTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATAccc                                                         >  1:1873471/1‑68 (MQ=255)

                    tGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGtt                                                <  1:3236871/68‑1 (MQ=255)

                    tGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGtt                                                <  1:2673144/68‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:3016842/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:1376178/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:351757/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:628501/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:1567492/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:1957197/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:632429/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:1784800/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:2852326/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:774175/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:2078355/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:966463/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:901125/69‑1 (MQ=255)

                          tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:221533/69‑1 (MQ=255)

                           gCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:2982622/68‑1 (MQ=255)

                           gCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg                                         <  1:356663/68‑1 (MQ=255)

                                 tCTTCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCag                                    <  1:2043049/67‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:843725/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:269696/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:1914880/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:1135163/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:1981044/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:722093/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:3241512/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCagag                                  <  1:323306/69‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCag                                    <  1:2748269/67‑1 (MQ=255)

                                 tCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCag                                    <  1:2265280/67‑1 (MQ=255)

                                   tGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGt                                 >  1:3080108/1‑68 (MQ=255)

                                       tCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              <  1:1481221/67‑1 (MQ=255)

                                       tCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTa                             <  1:1675965/68‑1 (MQ=255)

                                       tCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTa                             <  1:674818/68‑1 (MQ=255)

                                       tCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTa                             <  1:872650/68‑1 (MQ=255)

                                         tGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATa                                                            >  1:1627916/1‑35 (MQ=255)

                                         tGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATg                          >  1:2350791/1‑69 (MQ=255)

                                         tGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATg                          >  1:1117413/1‑69 (MQ=255)

                                         tGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATg                          >  1:1132880/1‑69 (MQ=255)

                                             tttGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              >  1:3177118/1‑61 (MQ=255)

                                             tttGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              >  1:1032947/1‑61 (MQ=255)

                                             tttGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              >  1:170270/1‑61 (MQ=255)

                                             tttGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              >  1:1939485/1‑61 (MQ=255)

                                             tttGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              >  1:2282702/1‑61 (MQ=255)

                                                   tCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGtt                                                <  1:3021564/37‑1 (MQ=255)

                                                     cGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTa                                >  1:126903/1‑51 (MQ=255)

                                                     cGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTa                                >  1:3155383/1‑51 (MQ=255)

                                                     cGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTa                                >  1:745468/1‑51 (MQ=255)

                                                     cGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTa                                >  1:2475341/1‑51 (MQ=255)

                                                             gctggGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              <  1:464799/45‑1 (MQ=255)

                                                             gctggGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTAtt                              >  1:1194149/1‑45 (MQ=255)

                                                                   tATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGc  >  1:373010/1‑67 (MQ=255)

                                                                   tATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGc  >  1:1473560/1‑67 (MQ=255)

                                                                   tATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGc  >  1:3271737/1‑67 (MQ=255)

                                                                   tATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGc  >  1:1843123/1‑67 (MQ=255)

                                                                   tATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGc  >  1:2825877/1‑67 (MQ=255)

                                                                   tATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGc  >  1:2196687/1‑67 (MQ=255)

                                                                   tATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGc  >  1:454037/1‑67 (MQ=255)

GATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTGTTCAGAGTATTAATGGGCTGTGCAAAGCCGACAAACGGC  >  minE/2640081‑2640214

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