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	2,867,123	G→A	P96L (CCG→CTG)	nlpD ←	predicted outer membrane lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,867,123	0	G	A	91.4%	101.4 / 1.7	35	P96L (CCG→CTG)	nlpD	predicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand): ref base G (2/1); new base A (6/26); total (8/27)
Fisher's exact test for biased strand distribution p-value = 1.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01

TAACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTG  >  W3110S.gb/2867057‑2867190

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:915918/71‑1 (MQ=255)

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:4060250/71‑1 (MQ=255)

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:4038176/71‑1 (MQ=255)

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:4033476/71‑1 (MQ=255)

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:322130/71‑1 (MQ=255)

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:2313128/71‑1 (MQ=255)

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:2727595/71‑1 (MQ=255)

taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg                                                                 <  1:2715626/71‑1 (MQ=255)

      cgtttCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc                                                           <  1:661692/69‑1 (MQ=255)

      ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGa                                                             <  1:3788227/69‑1 (MQ=255)

      ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc                                                           <  1:3185696/71‑1 (MQ=255)

      ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc                                                           <  1:2672252/71‑1 (MQ=255)

      ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc                                                           <  1:241030/71‑1 (MQ=255)

       cTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc                                                           <  1:2673474/70‑1 (MQ=255)

       cTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc                                                           <  1:740218/70‑1 (MQ=255)

                        tACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg                                                  <  1:3775995/62‑1 (MQ=255)

                                  tataGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgt                               >  1:3835593/1‑71 (MQ=255)

                                  tataGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgt                               >  1:1145407/1‑71 (MQ=255)

                                  tataGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgt                               >  1:496404/1‑71 (MQ=255)

                                  tataGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgt                               >  1:1527367/1‑71 (MQ=255)

                                  tataGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgt                               >  1:2843303/1‑71 (MQ=255)

                                  tataGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgt                               >  1:177481/1‑71 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:2489027/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:3376621/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:3319031/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:139248/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:465180/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:2129999/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:1322674/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:243603/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:1009583/63‑1 (MQ=255)

                                    taGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCAGAGCTACTGGCTGCACTGGCTGGAtt                                     <  1:325065/63‑1 (MQ=255)

                                                        cATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGCtt                                     <  1:1766878/43‑1 (MQ=38)

                                                                ccGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGctgctg  >  1:3662644/1‑70 (MQ=255)

                                                                ccGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGctgctg  >  1:662248/1‑70 (MQ=255)

TAACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTG  >  W3110S.gb/2867057‑2867190

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