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	1,889,608	G→A	57.3%	G207G (GGC→GGT)	gudX ←	predicted glucarate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,889,608	0	G	A	57.3%	18.5 / 56.6	75	G207G (GGC→GGT)	gudX	predicted glucarate dehydratase
Reads supporting (aligned to +/- strand): ref base G (16/16); new base A (16/27); total (32/43)
Fisher's exact test for biased strand distribution p-value = 3.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGCACA  >  minE/1889540‑1889668

cgcgCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACAcgccg                                                              >  1:1945194/1‑69 (MQ=255)

cgcgCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACAcgccg                                                              >  1:2027901/1‑69 (MQ=255)

        cGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAg                                                      <  1:3365871/69‑1 (MQ=255)

        cGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAg                                                      <  1:1516/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:1014941/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:988925/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:1851409/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:1690191/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:546929/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:1265817/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:3426864/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:2962003/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:2746502/69‑1 (MQ=255)

             aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:2680508/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:2274283/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:1912205/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:2626143/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:2476771/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:455526/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:559868/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:75562/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:867925/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:992880/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:1002739/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:1346495/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:1496985/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:1590900/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:167651/69‑1 (MQ=255)

              gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa                                                 <  1:2880919/68‑1 (MQ=255)

               cGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:3383804/68‑1 (MQ=255)

                gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt                                              <  1:3173458/69‑1 (MQ=255)

                gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt                                              <  1:1986301/69‑1 (MQ=255)

                gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt                                              <  1:2693399/69‑1 (MQ=255)

                gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt                                              <  1:96105/69‑1 (MQ=255)

                gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt                                              <  1:2547050/69‑1 (MQ=255)

                gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt                                              <  1:2254041/69‑1 (MQ=255)

                   tcttcAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa                                                <  1:216596/64‑1 (MQ=255)

                                             tCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCt                 >  1:2394368/1‑69 (MQ=255)

                                             tCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCt                 >  1:2281258/1‑69 (MQ=255)

                                             tCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCt                 >  1:1586982/1‑69 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:457755/69‑1 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:706768/69‑1 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:483431/69‑1 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:2774653/69‑1 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:1162617/69‑1 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:914502/69‑1 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:3164193/69‑1 (MQ=255)

                                                    cGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCa          <  1:3172187/69‑1 (MQ=255)

                                                        agctAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:1334607/4‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:1186298/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:698009/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:1098641/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:3433212/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:3213919/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:1077095/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:922914/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:3261186/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:3231460/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:185456/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:321171/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:2930304/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:2054691/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:1675898/1‑63 (MQ=255)

                                                        aGGTAACACGCCACCCTTAAGTTTGAAATCTTTAAAGCCATAGCGATCCTGTGAGGCTTCCGc            >  1:2466787/1‑63 (MQ=255)

                                                           tAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcac   >  1:39458/1‑69 (MQ=255)

                                                           tAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcac   >  1:1045337/1‑69 (MQ=255)

                                                           tAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcac   >  1:2026821/1‑69 (MQ=255)

                                                           tAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcac   >  1:2030698/1‑69 (MQ=255)

                                                           tAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcac   >  1:1666769/1‑69 (MQ=255)

                                                           tAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcac   >  1:1002420/1‑69 (MQ=255)

                                                           tAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcac   >  1:470848/1‑69 (MQ=255)

                                                            aaCACGCCGCCCTTAAGTTTGAGATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcaca  >  1:698855/1‑69 (MQ=255)

                                                            aaCACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcaca  >  1:813536/1‑69 (MQ=255)

                                                            aaCACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcaca  >  1:631311/1‑69 (MQ=255)

                                                            aaCACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcaca  >  1:537686/1‑69 (MQ=255)

                                                            aaCACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcaca  >  1:126029/1‑69 (MQ=255)

                                                            aaCACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGcaca  >  1:1827413/1‑69 (MQ=255)

CGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAATCTTTAAAGCCGTAGCGATCCTGTGAGGCTTCCGCCAGACGCACA  >  minE/1889540‑1889668

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