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	2,563,258	A→G	52.9%	R273R (CGT→CGC)	lldP ←	L‑lactate permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,563,258	0	A	G	52.9%	3.4 / 42.6	53	R273R (CGT→CGC)	lldP	L‑lactate permease
Reads supporting (aligned to +/- strand): ref base A (17/8); new base G (17/11); total (34/19)
Fisher's exact test for biased strand distribution p-value = 7.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGTAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAT  >  minE/2563192‑2563306

aGTGTAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACg                                                <  1:1751823/69‑1 (MQ=255)

aGTGTAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACg                                                <  1:1594524/69‑1 (MQ=255)

    tAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACt                                            >  1:3168196/1‑69 (MQ=255)

    tAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACt                                            >  1:293282/1‑69 (MQ=255)

    tAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACt                                            >  1:2679508/1‑69 (MQ=255)

    tAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACt                                            >  1:2670049/1‑69 (MQ=255)

    tAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACt                                            >  1:2390762/1‑69 (MQ=255)

    tAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACt                                            >  1:1678735/1‑69 (MQ=255)

    tAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCACCAAATCACCAAAACGGAATACACGCACt                                            >  1:1537212/1‑69 (MQ=255)

           tgtgGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGcc                                     >  1:768093/1‑69 (MQ=255)

           tgtgGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGc                                      >  1:2007057/1‑68 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:181453/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:3368507/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:1016775/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:640991/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:165382/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:96077/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:1522772/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:1147497/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:803413/64‑1 (MQ=255)

           tgtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:1492246/64‑1 (MQ=255)

            gtgAGCCAGCGTCATATCAACCTGTGACGCCCCTAAGTCACCGAAGCGGAATACGCGCACTgg                                          <  1:2084432/63‑1 (MQ=255)

                      gTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGa                            >  1:657541/1‑67 (MQ=255)

                      gTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAgg                          <  1:2671139/69‑1 (MQ=255)

                      gTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAgg                          >  1:2922130/1‑69 (MQ=255)

                            tCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAg                     >  1:385708/1‑68 (MQ=255)

                            tCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGc                    >  1:1304369/1‑69 (MQ=255)

                            tCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGc                    >  1:1240080/1‑69 (MQ=255)

                              aaCCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGc                    >  1:2264526/1‑67 (MQ=255)

                              aaCCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGc                    >  1:1932790/1‑67 (MQ=255)

                                      aCGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCag           >  1:2265145/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:511429/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:750828/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:754379/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:496878/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:2595515/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:3354651/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:731090/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:297779/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:1144460/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:131391/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:137612/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:1599262/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:1715631/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:2132249/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:2875769/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:295479/1‑68 (MQ=255)

                                          ccctAAGTCACCGAAGCGGAATACGCGCACTGGTTGCCAGCGTTTGAGGAACAGTGTCAGACAGAGCa       >  1:2995817/1‑68 (MQ=255)

                                              aaaTCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAt  <  1:630068/69‑1 (MQ=255)

                                              aaaTCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAt  <  1:567478/69‑1 (MQ=255)

                                              aaaTCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAt  <  1:1635502/69‑1 (MQ=255)

                                              aaaTCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAt  <  1:1260014/69‑1 (MQ=255)

                                              aaaTCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAt  <  1:855016/69‑1 (MQ=255)

                                                                 cacGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAt  >  1:1364478/1‑50 (MQ=255)

                                                                 cacGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAt  >  1:853723/1‑50 (MQ=255)

AGTGTAACCGGTGTGGGCCAGCGTCATATCAACCTGTGACGCCCCCAAATCACCAAAACGGAATACACGCACTGGCTGCCAGCGTTTGAGGAACAGCGTCAGGCAGAGCAGTGAT  >  minE/2563192‑2563306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A