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 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,244,320	C→T	100%	C113Y (TGC→TAC)	ldcA ←	L,D‑carboxypeptidase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,244,320	0	C	T	91.8%	170.2 / 6.4	61	C113Y (TGC→TAC)	ldcA	L,D‑carboxypeptidase A
Reads supporting (aligned to +/- strand): ref base C (0/5); new base T (30/26); total (30/31)
Fisher's exact test for biased strand distribution p-value = 5.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCGCCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGCACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGCCACC  >  W3110S.gb/1244254‑1244385

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:411612/71‑1 (MQ=255)

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:3399783/71‑1 (MQ=255)

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:2267902/71‑1 (MQ=255)

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:2125414/71‑1 (MQ=255)

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:1981434/71‑1 (MQ=255)

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:3672018/71‑1 (MQ=255)

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:3269930/71‑1 (MQ=255)

gcgcCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTg                                                               <  1:30188/71‑1 (MQ=255)

         tttGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCgg                                                       >  1:1088640/1‑70 (MQ=255)

         tttGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCgg                                                       >  1:1980139/1‑70 (MQ=255)

             cTACCAGCATGGGGCCGCTAAATGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTaaa                                                   <  1:1620467/70‑1 (MQ=255)

             cTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTaaa                                                   <  1:1013334/70‑1 (MQ=255)

             cTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTaaa                                                   <  1:1247894/70‑1 (MQ=255)

             cTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTaaa                                                   <  1:736827/70‑1 (MQ=255)

             cTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTaaa                                                   <  1:2662691/70‑1 (MQ=255)

             cTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTaaa                                                   <  1:1217064/70‑1 (MQ=255)

                 cAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGc                                              <  1:339087/71‑1 (MQ=255)

                 cAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGCACTGAATGGCGGTAAAATCGc                                              <  1:812112/71‑1 (MQ=255)

                  aGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGc                                              >  1:2940024/1‑70 (MQ=255)

                  aGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGc                                              >  1:2874412/1‑70 (MQ=255)

                      tGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGa                                                              <  1:392768/50‑1 (MQ=255)

                      tGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGa                                                              <  1:3660028/50‑1 (MQ=255)

                      tGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGa                                                              <  1:2412339/50‑1 (MQ=255)

                      tGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGCACTg                                                               <  1:2405618/49‑1 (MQ=255)

                      tGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGCACTg                                                               <  1:1959201/49‑1 (MQ=255)

                      tGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGCACTg                                                               <  1:1955603/49‑1 (MQ=255)

                       ggggCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:1182343/1‑46 (MQ=255)

                       ggggCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:3113428/1‑46 (MQ=255)

                       ggggCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGCACTg                                                               <  1:3381376/48‑1 (MQ=255)

                        gggCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAAt                                                            >  1:2335890/1‑50 (MQ=255)

                        gggCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAAt                                                            >  1:3222052/1‑50 (MQ=255)

                        gggCAGATAAAGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGAAt                                                            >  1:476715/1‑50 (MQ=255)

                                aaaGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGaa                                                             >  1:805132/1‑41 (MQ=255)

                                aaaGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGaa                                                             >  1:3292606/1‑41 (MQ=255)

                                aaaGGTGATGACATTGCCATGCGCCAGAAGACCGTACTGaa                                                             >  1:3300599/1‑41 (MQ=255)

                                 aaGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:2891630/1‑36 (MQ=255)

                                 aaGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:1920858/1‑36 (MQ=255)

                                 aaGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:3693827/1‑36 (MQ=255)

                                 aaGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:774022/1‑36 (MQ=255)

                                 aaGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:2226182/1‑36 (MQ=255)

                                 aaGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:448235/1‑36 (MQ=255)

                                 aaGGTGATGACATTGCCATGCGCCAGAAGACCGTAc                                                                 >  1:1289255/1‑36 (MQ=255)

                                            aTTGCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAt                   <  1:1686399/71‑1 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgtt                >  1:2790522/1‑71 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgtt                >  1:781033/1‑71 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgtt                >  1:344085/1‑71 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgtt                >  1:3419163/1‑71 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgtt                >  1:168871/1‑71 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgt                 >  1:2188923/1‑70 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtg                  >  1:1840671/1‑69 (MQ=255)

                                               gCCATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtg                  >  1:126326/1‑69 (MQ=255)

                                                ccATGCGCCAGAAGACCGTACTGAATGGCGTTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgtt                <  1:2707276/70‑1 (MQ=255)

                                                 cATGCGCCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCAtgttgt              <  1:2785725/71‑1 (MQ=255)

                                                     cgcCAGAAGACCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGc          >  1:2499610/1‑71 (MQ=255)

                                                     cgcCAGAAGACCGTACTGAATGGCGGTAAAATAGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGc          >  1:957606/1‑71 (MQ=255)

                                                         agaagaCCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGc      <  1:2917691/71‑1 (MQ=255)

                                                          gaagaCCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGc      >  1:352031/1‑70 (MQ=255)

                                                             gaCCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGccacc  <  1:2415996/71‑1 (MQ=255)

                                                             gaCCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGccacc  <  1:1984507/71‑1 (MQ=255)

                                                             gaCCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGccacc  <  1:819049/71‑1 (MQ=255)

                                                              aCCGTACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGccacc  <  1:2463131/70‑1 (MQ=255)

GCGCCAAAGTTTGCTACCAGCATGGGGCCGCTAAAGGTGATGACATTGCCATGCGCCAGAAGACCGCACTGAATGGCGGTAAAATCGCTATGTCCGCAAATGAGCAACGGGTCATGTTGTTGGCGAGCCACC  >  W3110S.gb/1244254‑1244385

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