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	1,960,798	G→A	70.5%	I217I (ATC→ATT)	pgk ←	phosphoglycerate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,960,798	0	G	A	70.5%	48.4 / 22.6	54	I217I (ATC→ATT)	pgk	phosphoglycerate kinase
Reads supporting (aligned to +/- strand): ref base G (14/2); new base A (21/17); total (35/19)
Fisher's exact test for biased strand distribution p-value = 3.03e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCGTACAGGGATTTACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTT  >  minE/1960745‑1960860

tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:2225184/1‑68 (MQ=255)

tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:2466392/1‑68 (MQ=255)

tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:1234488/1‑68 (MQ=255)

tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:575239/1‑68 (MQ=255)

tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:1562913/1‑68 (MQ=255)

tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:3220679/1‑68 (MQ=255)

tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:1691727/1‑68 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:437334/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:2080666/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:2709144/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:2765651/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:2785346/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:393127/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:1043693/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:548997/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:623079/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:777629/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:874896/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:904296/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:99090/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:1735814/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:1145789/69‑1 (MQ=255)

          aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:189097/69‑1 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCt                                          >  1:197121/1‑63 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:2474848/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:605161/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:267273/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:3058186/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:1813248/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:1489071/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:2961781/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                                     >  1:2956146/1‑68 (MQ=255)

             tACCCACATCGTGGCCTTGTGACGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGt                                       >  1:1925618/1‑66 (MQ=255)

                     tCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTa                            <  1:2709575/69‑1 (MQ=255)

                     tCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTa                            <  1:908313/69‑1 (MQ=255)

                       gTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                                       <  1:1702365/56‑1 (MQ=255)

                             ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAggg                     >  1:285083/1‑68 (MQ=255)

                             ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                    >  1:1424405/1‑69 (MQ=255)

                             ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                    >  1:1995758/1‑69 (MQ=255)

                             ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                    >  1:3052192/1‑69 (MQ=255)

                             ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                    >  1:2975565/1‑69 (MQ=255)

                             ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                    >  1:1777995/1‑69 (MQ=255)

                             ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa                    >  1:2529121/1‑69 (MQ=255)

                               gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:3074893/1‑37 (MQ=25)

                               gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:1568256/1‑37 (MQ=25)

                               gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:578727/1‑37 (MQ=25)

                               gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:637433/1‑37 (MQ=25)

                               gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:1122089/1‑37 (MQ=25)

                               gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:109126/1‑37 (MQ=25)

                               gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                                                 >  1:2036803/1‑37 (MQ=25)

                                                  aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt  >  1:130658/1‑66 (MQ=255)

                                                  aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt  >  1:631440/1‑66 (MQ=255)

                                                  aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt  >  1:2308715/1‑66 (MQ=255)

                                                  aGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGttt  >  1:1002837/1‑66 (MQ=255)

TCGTACAGGGATTTACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGAGTCCAGAACGGTCAGTTT  >  minE/1960745‑1960860

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