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 F28 I2 R2	356	55.1	4139924	95.4%	3949487	63.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	393,168	T→C	G310G (GGT→GGC)	yaiU →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	393,168	0	T	C	78.4%	75.4 / 16.7	37	G310G (GGT→GGC)	yaiU	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (8/0); new base C (6/23); total (14/23)
Fisher's exact test for biased strand distribution p-value = 7.78e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

ACGTCTTTGTTGATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCA  >  W3110S.gb/393098‑393235

acGTCTTTGTTGATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:3141066/71‑1 (MQ=255)

         ttgATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt                                                            <  1:61239/71‑1 (MQ=255)

         ttgATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt                                                            <  1:2138741/71‑1 (MQ=255)

         ttgATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt                                                            <  1:469953/71‑1 (MQ=255)

         ttgATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt                                                            <  1:1488144/71‑1 (MQ=255)

         ttgATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt                                                            <  1:3603521/71‑1 (MQ=255)

         ttgATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt                                                            <  1:1551797/71‑1 (MQ=255)

         ttgATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt                                                            <  1:161899/71‑1 (MQ=255)

               gTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGt                                                      <  1:2307610/71‑1 (MQ=255)

               gTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGt                                                      <  1:209313/71‑1 (MQ=255)

               gTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGt                                                      <  1:2035681/71‑1 (MQ=255)

               gTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGt                                                      <  1:2706812/71‑1 (MQ=255)

               gTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACCGCACTTACGTTGACGGt                                                      <  1:2683427/71‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGTAACGGt                                                                     <  1:532732/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:2791680/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:2969945/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:2635165/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:3864522/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:2561875/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:2487240/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:452846/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:2512810/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:1046856/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:1950597/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:863147/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:858456/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:882889/53‑1 (MQ=255)

                  gCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:1476850/53‑1 (MQ=255)

                    ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTAc                                                                   >  1:2036464/1‑53 (MQ=255)

                    ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTAc                                                                   >  1:2026399/1‑53 (MQ=255)

                    ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTAc                                                                   >  1:59200/1‑53 (MQ=255)

                    ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTAc                                                                   >  1:512695/1‑53 (MQ=255)

                    ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTAc                                                                   >  1:136965/1‑53 (MQ=255)

                    ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTAc                                                                   >  1:1546293/1‑53 (MQ=255)

                      gAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGt                                                                     <  1:3164499/49‑1 (MQ=255)

                                    tCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTgg                                 >  1:769049/1‑71 (MQ=255)

                                    tCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTgg                                 >  1:1474252/1‑71 (MQ=255)

                                    tCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTgg                                 >  1:4113118/1‑71 (MQ=255)

                                    tCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTgg                                 >  1:4112595/1‑71 (MQ=255)

                                    tCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTgg                                 >  1:2696267/1‑71 (MQ=255)

                                                  tCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGa                    >  1:3093437/1‑70 (MQ=255)

                                                    tGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAg                 >  1:1667125/1‑71 (MQ=255)

                                                    tGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAg                 >  1:186422/1‑71 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt            <  1:669987/71‑1 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt            <  1:904479/71‑1 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt            <  1:1202035/71‑1 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt            <  1:3277121/71‑1 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt            <  1:2045174/71‑1 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt            <  1:1860805/71‑1 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt            <  1:1290147/71‑1 (MQ=255)

                                                         ccATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGGTTGAAAGCCGGt            <  1:914820/71‑1 (MQ=255)

                                                                   cGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCa  <  1:622457/71‑1 (MQ=255)

                                                                   cGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCa  <  1:3713175/71‑1 (MQ=255)

                                                                   cGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCa  <  1:1491930/71‑1 (MQ=255)

ACGTCTTTGTTGATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTACGACTTCA  >  W3110S.gb/393098‑393235

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