BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472762.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,517,400 number of mapped reads = 15,398,552 (99.23%) number of supplementary alignments = 53,970 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,723,938 number of mapped paired reads (second in pair) = 7,674,614 number of mapped paired reads (both in pair) = 15,322,212 number of mapped paired reads (singletons) = 76,340 number of mapped bases = 1,517,878,169 bp number of sequenced bases = 1,517,680,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,508,946 duplication rate = 48.14% >>>>>>> Insert size mean insert size = 21,244.5279 std insert size = 1,439,761.5287 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 54.8284 >>>>>>> ACTG content number of A's = 425,167,734 bp (28.01%) number of C's = 335,564,812 bp (22.11%) number of T's = 422,968,852 bp (27.87%) number of G's = 333,683,108 bp (21.99%) number of N's = 296,038 bp (0.02%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,795,101 number of insertions = 87,155 mapped reads with insertion percentage = 0.56% number of deletions = 85,745 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.4903X std coverageData = 21.0269X There is a 3.91% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 168656131 0.6766528015992386 28.516885813050116 chr2 243199373 128734218 0.5293361426552691 23.88007591877039 chr3 198022430 212583953 1.0735347152340269 31.130909280102053 chr4 191154276 76056214 0.3978786956353516 15.369198273117075 chr5 180915260 89483755 0.4946169549213261 23.6375428271221 chr6 171115067 81946944 0.47889964008838565 16.651523253801567 chr7 159138663 53855591 0.3384192752706487 13.584674859164059 chr8 146364022 60794802 0.41536711802030146 20.676074856968707 chr9 141213431 106331036 0.7529810390344528 23.24907472385855 chr10 135534747 20613474 0.15208995815663418 9.014103725652502 chr11 135006516 72495356 0.5369767189607352 20.019426203420053 chr12 133851895 79862400 0.5966475110419617 23.88591679364092 chr13 115169878 34603620 0.3004572080904696 17.318808055886134 chr14 107349540 37112064 0.34571237100783103 25.702470982920246 chr15 102531392 43093175 0.42029249929621554 20.321400662134966 chr16 90354753 52817011 0.5845515509294791 19.66076209730734 chr17 81195210 50093011 0.616945396163148 19.137995463228584 chr18 78077248 16279848 0.20850950074469837 11.781015357484115 chr19 59128983 5097804 0.08621497853260895 2.736806101522297 chr20 63025520 3935151 0.062437422174382695 2.91839716814704 chr21 48129895 16852308 0.3501422141062223 30.29570168691451 chr22 51304566 5552305 0.10822243384731098 4.12629351915683 chrMT 16571 1471 0.08876953714320197 0.30843354883992097 chrX 155270560 100720258 0.6486758210957698 20.055826668990484 chrY 59373566 306269 0.005158339318881403 0.37868942462771393