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 F3 I0 R2	232	76.3	4135488	90.9%	3759158	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,004,302	G→A	25.5%	S483F (TCT→TTT)	hybC ←	hydrogenase 2, large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,004,302	0	G	A	25.5%	89.9 / 32.3	51	S483F (TCT→TTT)	hybC	hydrogenase 2, large subunit
Reads supporting (aligned to +/- strand): ref base G (23/15); new base A (7/6); total (30/21)
Fisher's exact test for biased strand distribution p-value = 7.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

TTCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGCT  >  minE/2004236‑2004371

ttCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:2792347/71‑1 (MQ=255)

ttCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:526805/71‑1 (MQ=255)

ttCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:4096393/71‑1 (MQ=255)

ttCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:1886707/71‑1 (MQ=255)

ttCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:1806099/71‑1 (MQ=255)

ttCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:3351350/71‑1 (MQ=255)

     ggTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCa                                                                 >  1:1173531/1‑68 (MQ=255)

             gAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCgcggc                                                      >  1:796717/1‑71 (MQ=255)

             gAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCgcggc                                                      >  1:1975740/1‑71 (MQ=255)

             gAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCgcggc                                                      >  1:3004542/1‑71 (MQ=255)

                        tGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:1032762/47‑1 (MQ=255)

                        tGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:2182522/47‑1 (MQ=255)

                        tGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:21685/47‑1 (MQ=255)

                        tGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:244455/47‑1 (MQ=255)

                        tGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:2675002/47‑1 (MQ=255)

                        tGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:1607632/47‑1 (MQ=255)

                        tGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGagagag                                                                   <  1:1086657/47‑1 (MQ=255)

                             gTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATAc                                                              <  1:3623195/47‑1 (MQ=255)

                             gTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCaa                                      <  1:1363944/71‑1 (MQ=255)

                               tGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAaca                                    >  1:768711/1‑71 (MQ=255)

                                gCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGc                                                                  >  1:1711227/1‑40 (MQ=255)

                                gCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGc                                                                  >  1:2677734/1‑40 (MQ=255)

                                gCTGATGAAACCGTCTTTAATAACCATCCAGTGAGAGAGc                                                                  >  1:2862085/1‑40 (MQ=255)

                                     tgatACCGTCTTTAATAACCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCttt                               >  1:1849045/1‑70 (MQ=255)

                                     tgatACAGTCTTTAATAACCATCCAGTGAAAGAGCATAC‑‑CGCGGCGCTTCGAGGAAGCCAACACCTTTGaa                            >  1:4091182/1‑71 (MQ=255)

                                      gatACCGTCTTTAATAACCATCCAGTGAGAGAGCAt                                                                >  1:2819245/1‑36 (MQ=255)

                                      gatACCGTCTTTAATAACCATCCAGTGAGAGAGCAt                                                                >  1:1983948/1‑36 (MQ=255)

                                      gatACCGTCTTTAATAACCATCCAGTGAGAGAGCAt                                                                >  1:716080/1‑36 (MQ=255)

                                      gatACCGTCTTTAATAACCATCCAGTGAGAGAGCAt                                                                >  1:2393396/1‑36 (MQ=255)

                                          ccGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTc                                                 <  1:767870/47‑1 (MQ=255)

                                          ccGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTc                                                 <  1:994658/47‑1 (MQ=255)

                                          ccGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTc                                                 <  1:1244379/47‑1 (MQ=255)

                                          ccGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAAtt                          <  1:239590/70‑1 (MQ=255)

                                          ccGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAAtt                          <  1:921205/70‑1 (MQ=255)

                                          ccGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAAtt                          <  1:2185598/70‑1 (MQ=255)

                                             tCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCttg                               <  1:3292371/62‑2 (MQ=255)

                                             tCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTg                              <  1:1056342/63‑1 (MQ=255)

                                             tCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTg                              <  1:287550/63‑1 (MQ=255)

                                             tCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTg                              <  1:2136103/63‑1 (MQ=255)

                                             tCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTg                              <  1:3209439/63‑1 (MQ=255)

                                             tCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTg                              <  1:1866150/63‑1 (MQ=255)

                                               tttAATAACCATCCAGTGAGAGAGAATACCGCGCGGCGCTTCGAGGaa                                           >  1:2153782/1‑48 (MQ=255)

                                                 taataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCg                                                >  1:2507516/1‑41 (MQ=255)

                                                 taataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCAccc                     >  1:1192246/1‑68 (MQ=255)

                                                 taataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGtt                  >  1:1574120/1‑71 (MQ=255)

                                                 taataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGtt                  >  1:1461672/1‑71 (MQ=255)

                                                 taataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGtt                  >  1:1793950/1‑71 (MQ=255)

                                                 taataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGtt                  >  1:295081/1‑71 (MQ=255)

                                                 taataaCCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGcc                                        >  1:1244942/1‑49 (MQ=255)

                                                 taataaCCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGcc                                        >  1:2115773/1‑49 (MQ=255)

                                                 taataaCCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGcc                                        >  1:1074670/1‑49 (MQ=255)

                                                 taataaCCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCAccc                     <  1:2991761/68‑1 (MQ=255)

                                                 taataaCCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCAccc                     <  1:3868552/68‑1 (MQ=255)

                                                 taataaCCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCg                    >  1:85568/1‑69 (MQ=255)

                                                  aataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTg                 >  1:3588732/1‑71 (MQ=255)

                                                  aataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTg                 >  1:911319/1‑71 (MQ=255)

                                                  aataaCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTg                 >  1:3128860/1‑71 (MQ=255)

                                                  aataaCCATCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCaa                                      >  1:1104451/1‑50 (MQ=255)

                                                      aCCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCgg             <  1:2918271/71‑1 (MQ=255)

                                                        cATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGaa           <  1:1560612/71‑1 (MQ=255)

                                                         aTCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGaa           <  1:2099719/70‑1 (MQ=255)

                                                         aTCCAGTGAAAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGaa           <  1:871335/70‑1 (MQ=255)

                                                            cAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGaa                            >  1:2961884/1‑50 (MQ=255)

                                                               tGAAAGAGCATACCGCGCTGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGaa           <  1:1922583/64‑1 (MQ=255)

                                                                gagagaGCATACCGCGCGGCGCTTCGAGGAAG‑CAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGCt  >  1:967084/1‑71 (MQ=255)

                                                                 agagagCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAAtt                          >  1:3792683/1‑47 (MQ=255)

                                                                 agagagCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGCt  >  1:1922444/1‑71 (MQ=255)

                                                                 agagagCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGCt  >  1:244306/1‑71 (MQ=255)

TTCCAGGTTGATGGAACAACCGCCTGGTAGTTGCTGATGATACCGTCTTTAATAACCATCCAGTGAGAGAGCATACCGCGCGGCGCTTCGAGGAAGCCAACACCTTTGAATTCACCCGTTGCCGGAATGTTCGGCT  >  minE/2004236‑2004371

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