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	1,676,004	G→A	59.7%	S322S (AGC→AGT)	yfgB ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,676,004	0	G	A	59.7%	21.1 / 43.1	62	S322S (AGC→AGT)	yfgB	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (15/10); new base A (16/21); total (31/31)
Fisher's exact test for biased strand distribution p-value = 3.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

ATAGTGGTGAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTACACGGCGTATC  >  minE/1675945‑1676069

aTAGTGGTGAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCa                                                          <  1:2045576/69‑1 (MQ=255)

aTAGTGGTGAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCa                                                          <  1:2538921/69‑1 (MQ=255)

aTAGTGGTGAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCa                                                          <  1:3094832/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:2197345/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:297040/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:1721598/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:1617371/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:2066209/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:3261797/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:1289173/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:1160860/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:460518/69‑1 (MQ=255)

        gAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:568811/69‑1 (MQ=255)

                aGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGa                                          <  1:3238959/69‑1 (MQ=255)

                aGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGa                                          <  1:3318144/69‑1 (MQ=255)

                       caGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACTGCGCACCCGGGAACggg                                     <  1:3036842/67‑1 (MQ=255)

                       caGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACggg                                     <  1:933637/67‑1 (MQ=255)

                        aGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGgc                                                    >  1:3056666/1‑51 (MQ=255)

                        aGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTc                                  >  1:2967876/1‑69 (MQ=255)

                        aGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTc                                  >  1:2492572/1‑69 (MQ=255)

                        aGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTc                                  >  1:2742403/1‑69 (MQ=255)

                        aGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTc                                  >  1:1075366/1‑69 (MQ=255)

                        aGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTc                                  >  1:1107058/1‑69 (MQ=255)

                        aGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTc                                  >  1:1576812/1‑69 (MQ=255)

                            cTTTTGAGACACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCAc                               >  1:860885/1‑68 (MQ=255)

                            cTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCAc                               >  1:682015/1‑68 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATa                                                        >  1:2429586/1‑41 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:3073100/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:1074276/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:885035/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:1123901/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:134190/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:3156954/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:3141295/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:2181136/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:303817/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:1711220/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:2958262/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:2287504/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:2895728/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:106934/1‑42 (MQ=255)

                              tttGAGAAACGGTCGATACGGCTGTTCGAACTGCGTCCATAc                                                       >  1:254987/1‑42 (MQ=255)

                                 gagaAACGGGCGATACGGCTGTTCGAACTGCGTCCATACGgcgc                                                  <  1:526233/44‑1 (MQ=38)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATCCGGCGCGCCAGGGAACGGGTTCCACg                              <  1:782766/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:2548081/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:2193321/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:580164/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:556276/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:2046778/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:17653/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:136352/61‑1 (MQ=255)

                                    aaaCGGTCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:1568539/61‑1 (MQ=255)

                                    aaaCGATCGATACGGCTGTTCGAACTGCGTCCATACGGCGCGCCAGGGAACGGGTTCCACg                              <  1:644026/61‑1 (MQ=255)

                                      aCGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACg                                       <  1:2032067/50‑1 (MQ=255)

                                          tCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACg                                       <  1:2162687/46‑1 (MQ=255)

                                              tACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTa             <  1:2525501/68‑1 (MQ=255)

                                                        cGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGAt                 >  1:2913481/1‑54 (MQ=255)

                                                        cGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTACACGGCGTa    >  1:3164310/1‑67 (MQ=255)

                                                        cGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTACACGGCGTATc  >  1:392173/1‑69 (MQ=255)

                                                        cGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTACACGGCGTATc  >  1:2846440/1‑69 (MQ=255)

                                                        cGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTACACGGCGTATc  >  1:2060447/1‑69 (MQ=255)

                                                        cGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTACACGGCGTATc  >  1:3084257/1‑69 (MQ=255)

ATAGTGGTGAAACCGTAGCTCATCAGCACTTTTGAGAAACGGTCGATACGGCTGTTCGAGCTGCGTCCATACGGCGCACCCGGGAACGGGTTCCACGGGATCAGGTTGATCTTACACGGCGTATC  >  minE/1675945‑1676069

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