BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124957.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,053,000 number of mapped reads = 5,848,977 (96.63%) number of supplementary alignments = 5,731 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,980,246 number of mapped paired reads (second in pair) = 2,868,731 number of mapped paired reads (both in pair) = 5,718,578 number of mapped paired reads (singletons) = 130,399 number of mapped bases = 364,611,417 bp number of sequenced bases = 364,468,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 426,729 duplication rate = 5.02% >>>>>>> Insert size mean insert size = 25,658.1939 std insert size = 1,510,694.468 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 51.8337 >>>>>>> ACTG content number of A's = 100,708,955 bp (27.63%) number of C's = 64,578,406 bp (17.72%) number of T's = 110,302,075 bp (30.26%) number of G's = 88,876,372 bp (24.39%) number of N's = 3,167 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,386,986 number of insertions = 37,438 mapped reads with insertion percentage = 0.64% number of deletions = 97,503 mapped reads with deletion percentage = 1.65% homopolymer indels = 49.49% >>>>>>> Coverage mean coverageData = 0.1178X std coverageData = 1.0321X There is a 8.82% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 29862058 0.11980735646793032 1.4709779984766642 chr2 243199373 31545125 0.12970890759656686 1.0930703921434222 chr3 198022430 22621615 0.11423763964516545 0.4196129204955169 chr4 191154276 16310036 0.08532394012467709 0.44624569149709564 chr5 180915260 19633414 0.10852270836633682 0.4050197311384366 chr6 171115067 21318884 0.12458800019053845 0.8399670566740004 chr7 159138663 19342581 0.12154545372798564 1.3890326063026703 chr8 146364022 23373661 0.1596953997342325 0.6506259478752777 chr9 141213431 14469758 0.10246729293051451 0.8622457496597583 chr10 135534747 16939599 0.12498344059328195 2.3793780359705767 chr11 135006516 24085125 0.17839972257339046 0.8928829607054941 chr12 133851895 11767370 0.08791336125648426 0.3680406622744967 chr13 115169878 19369692 0.16818366344019223 0.696002985734739 chr14 107349540 5875285 0.0547304161713222 0.3535944005537852 chr15 102531392 7721099 0.07530473203757929 0.3511477405921122 chr16 90354753 10872542 0.12033171071808475 1.8553172768266233 chr17 81195210 7627262 0.09393733940709063 1.119426922437792 chr18 78077248 10279314 0.13165569052843665 1.3975983467121629 chr19 59128983 5516202 0.0932910007939761 1.102013809477931 chr20 63025520 9176341 0.1455972279165646 0.4829317685399538 chr21 48129895 3124437 0.06491676327155918 0.35349445971560706 chr22 51304566 2469227 0.04812879617771253 0.2607927971431287 chrMT 16571 112948 6.8160038621688495 5.762880371041209 chrX 155270560 30487318 0.19634963640241912 0.8659199073713025 chrY 59373566 710524 0.011967009022163163 0.45787490075548487