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 F3 I0 R1	560	56.4	4650532	94.9%	4413354	59.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,639,860	T→C	18.7%	intergenic (‑37/+309)	ynfN ← / ← cspI	hypothetical protein/cold shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,639,860	0	T	C	18.7%	103.3 / 18.9	48	intergenic (‑37/+309)	ynfN/cspI	hypothetical protein/cold shock protein
Reads supporting (aligned to +/- strand): ref base T (23/16); new base C (4/5); total (27/21)
Fisher's exact test for biased strand distribution p-value = 4.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

TGTGTTTTTTCGCCATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCG  >  W3110S.gb/1639792‑1639927

tgtgtTTTTTCGCCATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCActgc                                                                   <  1:1376906/71‑1 (MQ=255)

tgtgtTTTTTCGCCATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCAccgc                                                                   <  1:2458265/71‑1 (MQ=255)

    ttttttCGCCATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGt                                                               >  1:2034076/1‑71 (MQ=255)

                 tGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTaaaa                                                   <  1:4499631/70‑1 (MQ=255)

                  ggATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTaaaaa                                                  <  1:1309357/70‑1 (MQ=255)

                  ggATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTaaaaa                                                  <  1:168447/70‑1 (MQ=255)

                    atatTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAAc                                               <  1:3203831/71‑1 (MQ=255)

                      atTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTa                                             >  1:2447586/1‑71 (MQ=255)

                       ttCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCATCGCTGGTTCAGAGTTaaaaa                                                  <  1:859938/65‑1 (MQ=255)

                       ttCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTa                                             <  1:2747373/70‑1 (MQ=255)

                        tCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACCGCTGGTTCAGAGTTaaaaa                                                  <  1:4430283/64‑1 (MQ=255)

                            gCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGAttt                                       <  1:2291989/71‑1 (MQ=255)

                              atgatgGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCaga                                                          >  1:3725129/1‑50 (MQ=255)

                              atgatgGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGAttttt                                     <  1:2494837/71‑1 (MQ=255)

                               tgatgGTGTTAACTCCAGTCATCGCTGGCACTACCACCGCTGGTTCAGAGTTaaaaa                                                  <  1:4309726/57‑1 (MQ=255)

                                 atgCTGTTAACTCCAGTCATCGCTGGCACTACCACCTCTGGTTCAGAGTTaaaaaaa                                                >  1:4353609/1‑57 (MQ=255)

                                   ggTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCat                                >  1:4386837/1‑71 (MQ=255)

                                        tAACTCCAGTCATCGCTGGCACTACCACCGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGt                           >  1:2727305/1‑71 (MQ=255)

                                         aaCTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGt                           >  1:2517277/1‑70 (MQ=255)

                                         aaCTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGt                           >  1:766215/1‑70 (MQ=255)

                                             ccAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTaaaaaaa                                                >  1:3804748/1‑45 (MQ=255)

                                             ccAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCg                      >  1:886485/1‑71 (MQ=255)

                                             ccACTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCg                      >  1:4339953/1‑71 (MQ=255)

                                              cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATg                                           >  1:916423/1‑49 (MQ=255)

                                              cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATg                                           >  1:4021924/1‑49 (MQ=255)

                                              cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCg                      <  1:475708/70‑1 (MQ=255)

                                                gTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTaaaaa                                                  <  1:2925784/40‑1 (MQ=255)

                                                 tCATCGCTGGCACTACCACTGCTGGTTCAGAGTTaaa                                                    >  1:3754511/1‑37 (MQ=255)

                                                 tCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCatgat                             <  1:1079300/60‑1 (MQ=255)

                                                 tCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCgtag                   >  1:2778569/1‑70 (MQ=255)

                                                  cATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGAtttttt                                    >  1:4559680/1‑52 (MQ=255)

                                                  cATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTa                         >  1:4059512/1‑63 (MQ=255)

                                                  cATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTa                         >  1:1511597/1‑63 (MQ=255)

                                                   aTCGCTGGCACTACCACTGCTGGTTCAGAGTTaaaaaaa                                                >  1:4539470/1‑39 (MQ=255)

                                                   aTCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCgtagta                 <  1:3776196/70‑1 (MQ=255)

                                                   aTCGCTGGCACTACCACCGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTAt                >  1:3469528/1‑71 (MQ=255)

                                                    tCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGAttttt                                     <  1:2321700/49‑1 (MQ=255)

                                                    tCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTAtg               <  1:3504190/71‑1 (MQ=255)

                                                     cGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTAtgt              >  1:2480321/1‑71 (MQ=255)

                                                      gCTGGCACTACCACCGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTAtgtg             <  1:411691/71‑1 (MQ=255)

                                                          gCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAg           <  1:443233/69‑1 (MQ=255)

                                                          gCACTACCACCGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTa         <  1:1513429/71‑1 (MQ=255)

                                                            aCTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATc       <  1:1979812/71‑1 (MQ=255)

                                                             cTACCACTTCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATc       >  1:2836813/1‑70 (MQ=255)

                                                              tACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCat                                <  1:741826/44‑1 (MQ=255)

                                                               aCCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTc                                  >  1:2926979/1‑41 (MQ=255)

                                                               aCCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCgtagt                  >  1:808878/1‑57 (MQ=255)

                                                                ccACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTAc                        >  1:2947009/1‑50 (MQ=255)

                                                                 cACCGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCg                      >  1:1735907/1‑51 (MQ=255)

                                                                  aCTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCg  >  1:3025519/1‑70 (MQ=255)

                                                                   ctgctgGTTCAGAGTTAAAAAAACTATGAttttttt                                   <  1:2940017/36‑1 (MQ=255)

                                                                   ctgctgGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTAtgt              <  1:1595691/57‑1 (MQ=255)

TGTGTTTTTTCGCCATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCG  >  W3110S.gb/1639792‑1639927

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