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
A1 F21 I0 R2	308	27.9	1975068	96.7%	1909890	67.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,906,931	A→G	57.5%	V464V (GTT→GTC)	pyrG ←	CTP synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,906,931	0	A	G	57.5%	24.9 / 56.3	47	V464V (GTT→GTC)	pyrG	CTP synthetase
Reads supporting (aligned to +/- strand): ref base A (15/5); new base G (8/19); total (23/24)
Fisher's exact test for biased strand distribution p-value = 3.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GCAGACCTGCATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTGG  >  W3110S.gb/2906864‑2906985

gcAGACCTGCATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTcgaca                                                     <  1:1879033/71‑1 (MQ=255)

gcAGACCTGCATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTcgaca                                                     <  1:1374142/71‑1 (MQ=255)

gcAGACCTGCATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTcgaca                                                     <  1:1488472/71‑1 (MQ=255)

         cATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGgc                                            >  1:1690699/1‑71 (MQ=255)

         cATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGgc                                            >  1:1857198/1‑71 (MQ=255)

         cATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGgc                                            >  1:421751/1‑71 (MQ=255)

         cATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGgc                                            >  1:301371/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:1826183/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:1768701/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:1833396/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:1557246/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:204783/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:1534932/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:1297703/1‑71 (MQ=255)

             ttCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCAt                                        >  1:869601/1‑71 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:345629/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:22307/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:34686/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:456861/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:514828/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:804210/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:980637/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:1071535/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:1731819/70‑1 (MQ=255)

                aaTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:1547770/70‑1 (MQ=255)

                 aTCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTg                                      <  1:256941/69‑1 (MQ=255)

                           aCAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGa                          <  1:1097932/71‑1 (MQ=255)

                           aCAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGa                          <  1:794983/71‑1 (MQ=255)

                              gCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAAc                        >  1:1261851/1‑70 (MQ=255)

                                   ttgttgACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAgg                    >  1:128643/1‑69 (MQ=255)

                                   ttgttgACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGc                   >  1:1827639/1‑70 (MQ=255)

                                   ttgttgACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGc                   >  1:882206/1‑70 (MQ=255)

                                    tgttgACTTCGTAACGGTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCt                  <  1:1651462/70‑1 (MQ=255)

                                     gttgACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTAt                >  1:642495/1‑71 (MQ=255)

                                                 aCGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTAGAGCTGGCGAACCAGGCTATCGTCAACCAACt    >  1:383237/1‑71 (MQ=255)

                                                 aCGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGaa                         >  1:1675851/1‑50 (MQ=255)

                                                 aCGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACt    >  1:1555763/1‑71 (MQ=255)

                                                 aCGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACt    >  1:977134/1‑71 (MQ=255)

                                                 aCGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACt    >  1:1182338/1‑71 (MQ=255)

                                                 aCGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACt    >  1:118162/1‑71 (MQ=255)

                                                   ggTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:1497246/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:1315277/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:40580/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:1021394/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:389630/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:962555/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:1180290/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:1928045/71‑1 (MQ=255)

                                                   ggTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTgg  <  1:188977/71‑1 (MQ=255)

                                                        cGATGACGCTCGACAATTGTCGGCGCATTGTACAGCTGGCGa                          <  1:994298/42‑1 (MQ=255)

GCAGACCTGCATCTTCAATCTGTTTCAACAGCATGTTGTTGACTTCGTAACGGTGACGATGACGCTCAACAATTGTCGGCGCATTGTACAGCTGGCGAACCAGGCTATCGTCAACCAACTGG  >  W3110S.gb/2906864‑2906985

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