BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695921.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,946,536 number of mapped reads = 1,940,213 (99.68%) number of supplementary alignments = 55,992 (2.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 971,236 number of mapped paired reads (second in pair) = 968,977 number of mapped paired reads (both in pair) = 1,936,618 number of mapped paired reads (singletons) = 3,595 number of mapped bases = 289,101,874 bp number of sequenced bases = 289,017,331 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,520 duplication rate = 0.27% >>>>>>> Insert size mean insert size = 64,051.9089 std insert size = 2,478,298.4549 median insert size = 288 >>>>>>> Mapping quality mean mapping quality = 54.3975 >>>>>>> ACTG content number of A's = 85,257,950 bp (29.5%) number of C's = 59,105,076 bp (20.45%) number of T's = 84,773,185 bp (29.33%) number of G's = 59,845,484 bp (20.71%) number of N's = 35,636 bp (0.01%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,080,395 number of insertions = 34,571 mapped reads with insertion percentage = 1.73% number of deletions = 32,519 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.0934X std coverageData = 0.3537X There is a 7.86% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 25874274 0.10380826292906208 0.37628722836441125 chr2 243199373 35958390 0.14785560322970076 0.4512195312729242 chr3 198022430 20156229 0.1017876055757926 0.3565884878290186 chr4 191154276 15549897 0.08134736677300382 0.3368323786286553 chr5 180915260 21368215 0.11811173363706301 0.38623391225807113 chr6 171115067 18894619 0.11042054525800467 0.3742095875447818 chr7 159138663 14782737 0.0928921779366715 0.34425041088899394 chr8 146364022 6324600 0.043211438942283235 0.233258131606195 chr9 141213431 14727893 0.10429527061062627 0.3702149788026127 chr10 135534747 10973559 0.08096491300492854 0.3248637312834085 chr11 135006516 12478309 0.0924274573532436 0.34344887626584303 chr12 133851895 18426782 0.1376654547924032 0.41754364454568516 chr13 115169878 9320743 0.08093038876015828 0.3201850438816154 chr14 107349540 11178664 0.10413331999373263 0.3655388606540809 chr15 102531392 5948789 0.058019196696363975 0.2715095426153492 chr16 90354753 6409370 0.07093561530736518 0.32284640129292186 chr17 81195210 5632813 0.06937371059204109 0.2993955824937199 chr18 78077248 10352487 0.13259287776126535 0.4154032186846963 chr19 59128983 5100669 0.08626343192812905 0.33334376056622494 chr20 63025520 5171001 0.08204614575175262 0.3207915023234829 chr21 48129895 3139342 0.06522644605811004 0.3443141352397916 chr22 51304566 2927577 0.0570626988638789 0.2739669197065352 chrMT 16571 256569 15.483012491702372 6.507855516163111 chrX 155270560 6038906 0.038892794616056 0.22298306314906177 chrY 59373566 2109440 0.035528268590099506 0.23411294229889276