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	2,482,270	C→T	27.4%	S198S (TCG→TCA)	mdtL ←	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,482,270	0	C	T	27.4%	63.1 / 20.7	58	S198S (TCG→TCA)	mdtL	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base C (19/23); new base T (4/12); total (23/35)
Fisher's exact test for biased strand distribution p-value = 2.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGCGGGGGC  >  minE/2482204‑2482311

aGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGa                                         >  1:1175383/1‑69 (MQ=255)

aGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGa                                         >  1:3063741/1‑69 (MQ=255)

aGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGa                                         >  1:2332324/1‑69 (MQ=255)

         cACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAACCGGTTAAGCAGTGACTCGCTAtt                                >  1:584686/1‑69 (MQ=255)

         cACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAACCGGTTAAGCAGTGACTCGCTAtt                                >  1:557914/1‑69 (MQ=255)

         cACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAACCGGTTAAGCAGTGACTCGCTAtt                                >  1:2437668/1‑69 (MQ=255)

         cACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAACCGGTTAAGCAGTGACTCGCTAt                                 >  1:2464514/1‑68 (MQ=255)

         cACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTAtt                                >  1:1723446/1‑69 (MQ=255)

                     gAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGttt                    <  1:2940164/69‑1 (MQ=255)

                     gAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGttt                    <  1:2956887/69‑1 (MQ=255)

                     gAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGttt                    <  1:219820/69‑1 (MQ=255)

                     gAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGttt                    <  1:3397205/69‑1 (MQ=255)

                     gAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGttt                    <  1:904602/69‑1 (MQ=255)

                         gtggtgATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATcc                <  1:1970604/69‑1 (MQ=255)

                         gtggtgATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATcc                <  1:2346173/69‑1 (MQ=255)

                         gtggtgATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATcc                <  1:1641972/69‑1 (MQ=255)

                         gtggtgATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATcc                <  1:678493/69‑1 (MQ=255)

                            gtgATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGaa             >  1:1621028/1‑69 (MQ=255)

                              gATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGc           <  1:2074823/69‑1 (MQ=255)

                              gATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGc           <  1:2805325/69‑1 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATcc                <  1:431761/63‑1 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGc           >  1:122533/1‑68 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCt          >  1:428201/1‑69 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCt          >  1:1068315/1‑69 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCt          >  1:534834/1‑69 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCt          >  1:754244/1‑69 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCt          >  1:2696632/1‑69 (MQ=255)

                               aTAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGATATTTTCTCGTGGTTTATCCGAAGCt          >  1:1488553/1‑69 (MQ=255)

                                 aacaacACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTtctc                           <  1:3236166/50‑1 (MQ=255)

                                 aacaacACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        <  1:259402/69‑1 (MQ=255)

                                 aacaacACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        >  1:2801323/1‑69 (MQ=255)

                                 aacaacACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        <  1:2117345/69‑1 (MQ=255)

                                 aacaacACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        <  1:3102952/69‑1 (MQ=255)

                                 aacaacACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        >  1:3099881/1‑69 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGa              <  1:2673332/62‑1 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGa              <  1:2201608/62‑1 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        <  1:2744763/68‑1 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        <  1:2167016/68‑1 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        <  1:2856963/68‑1 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGc        <  1:2208445/68‑1 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGCg       >  1:944372/1‑69 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGCg       >  1:1242509/1‑69 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGCg       >  1:3371213/1‑69 (MQ=255)

                                  acaacaCGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGCg       >  1:3057937/1‑69 (MQ=255)

                                       acGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGCGGGGGc  >  1:2677657/1‑69 (MQ=255)

                                               ggAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGa              <  1:928044/49‑1 (MQ=255)

                                                  aaaacCTGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:3303664/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:2884773/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:2824119/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:1996437/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:1907851/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:2740910/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:2719513/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:1198889/46‑1 (MQ=255)

                                                  aaaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:1027772/46‑1 (MQ=255)

                                                   aaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:2175236/45‑1 (MQ=255)

                                                   aaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:2454630/45‑1 (MQ=255)

                                                   aaacCGGTTAAGCAGTGACTCGCTATTTTCTCGTGGTTTGTCCGa              <  1:1092945/45‑1 (MQ=255)

AGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAAAACGGTTAAGCAGCGACTCGCTATTTTCTCGTGGTTTATCCGAAGCTGCGGGGGC  >  minE/2482204‑2482311

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