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	693,657	G→A	49.2%	V70V (GTG→GTA)	hyaF →	protein involved in nickel incorporation into hydrogenase‑1 proteins

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	693,657	0	G	A	49.2%	‑2.4 / 53.8	61	V70V (GTG→GTA)	hyaF	protein involved in nickel incorporation into hydrogenase‑1 proteins
Reads supporting (aligned to +/- strand): ref base G (28/3); new base A (15/15); total (43/18)
Fisher's exact test for biased strand distribution p-value = 6.92e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATTGCGCTGTTAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGG  >  minE/693594‑693719

gATTGCGCTGTTAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGc                                                           >  1:2229398/1‑69 (MQ=255)

           tAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCt                                                  >  1:1623601/1‑67 (MQ=255)

           tAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCt                                                  >  1:1072317/1‑67 (MQ=255)

           tAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTg                                                 >  1:2142467/1‑68 (MQ=255)

           tAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTg                                                 >  1:646116/1‑68 (MQ=255)

           tAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTg                                                 >  1:1543876/1‑68 (MQ=255)

           tAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTg                                                 >  1:233264/1‑68 (MQ=255)

           tAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTg                                                 >  1:141301/1‑68 (MQ=255)

                  gTTACAACATCAACTAAGCGAACGCCAACGGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAtc                                          >  1:584525/1‑68 (MQ=255)

                  gTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAtc                                          >  1:272596/1‑68 (MQ=255)

                  gTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAtc                                          >  1:887590/1‑68 (MQ=255)

                  gTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAtc                                          >  1:832982/1‑68 (MQ=255)

                  gTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAtc                                          >  1:3327545/1‑68 (MQ=255)

                  gTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAtc                                          >  1:1687840/1‑68 (MQ=255)

                  gTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAAtc                                          >  1:633939/1‑68 (MQ=255)

                     acaacaTCAACTAAGCGAACGCCAACCGCCTTTGGGCGAGGTGCTGGCAGTCGa                                                     <  1:1200666/54‑1 (MQ=255)

                      caacaTCAACTAAGCGAACGCCAACTGCCGTTGGGCGAGGTGCTGGCAGTCGa                                                     <  1:1726861/53‑1 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTg                                                                >  1:1290441/1‑40 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:427667/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:452751/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:373078/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:458949/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:1567423/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:1722943/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:1481182/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:2427610/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:107120/1‑68 (MQ=255)

                        acaTCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACg                                    >  1:1050904/1‑68 (MQ=255)

                          aTCAACTAAGCGAACGCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCcg                                 <  1:1057264/69‑1 (MQ=255)

                          aTCAACTAAGCGAACGCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCcg                                 <  1:2912973/69‑1 (MQ=255)

                          aTCAACTAAGCGAACGCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCcg                                 <  1:2669520/69‑1 (MQ=255)

                          aTCAACTAAGCGAACGCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCcg                                 <  1:1809317/69‑1 (MQ=255)

                          aTCAACTAAGCGAACGCCAGCCGCCGCTGGGTGAGGTACTGGCAGGCGATCTGTTAAATCTCAACGCcg                                 <  1:2558820/69‑1 (MQ=255)

                             aaCTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCt                                                  >  1:1258317/1‑49 (MQ=255)

                             aaCTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCcgacg                              >  1:2805516/1‑69 (MQ=255)

                             aaCTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCcgacg                              >  1:919163/1‑69 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:2971070/69‑1 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:935322/69‑1 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:961046/69‑1 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:2308836/69‑1 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:1203056/69‑1 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:2155876/69‑1 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:2571749/69‑1 (MQ=255)

                                         gCCAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:1793671/69‑1 (MQ=255)

                                          ccAGCCGCCGCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:3427674/68‑1 (MQ=255)

                                            agccgccgCTGGGTGAGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTa                  <  1:1442835/64‑1 (MQ=255)

                                                      gggCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTtc      <  1:1480789/68‑1 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGTCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:2176510/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1934618/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1060084/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1563482/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1567612/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1756697/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1775428/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1785104/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:186534/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:3369760/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:1965112/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:212894/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:2906248/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:2868070/1‑67 (MQ=255)

                                                           aGGTACTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCgg  >  1:2503582/1‑67 (MQ=255)

GATTGCGCTGTTAAACGAGTTACAACATCAACTAAGCGAACGCCAACCGCCGTTGGGCGAGGTGCTGGCAGTCGATCTGTTAAATCTCAACGCCGACGATCGTCACTTTATCAATACGCTTCTCGG  >  minE/693594‑693719

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