BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006140.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 15,642,640 number of mapped reads = 13,532,011 (86.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,886,148 number of mapped paired reads (second in pair) = 6,645,863 number of mapped paired reads (both in pair) = 12,317,208 number of mapped paired reads (singletons) = 1,214,803 number of mapped bases = 522,131,202 bp number of sequenced bases = 522,072,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,210,295 duplication rate = 8.11% >>>>>>> Insert size mean insert size = 63,295.5914 std insert size = 2,479,515.8997 median insert size = 92 >>>>>>> Mapping quality mean mapping quality = 46.8388 >>>>>>> ACTG content number of A's = 142,156,394 bp (27.23%) number of C's = 113,439,753 bp (21.73%) number of T's = 147,069,092 bp (28.17%) number of G's = 119,384,710 bp (22.87%) number of N's = 23,016 bp (0%) GC percentage = 44.6% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,586,277 number of insertions = 17,736 mapped reads with insertion percentage = 0.13% number of deletions = 46,182 mapped reads with deletion percentage = 0.34% homopolymer indels = 45.8% >>>>>>> Coverage mean coverageData = 0.1687X std coverageData = 0.8514X There is a 7.88% of reference with a coverageData >= 1X There is a 4.11% of reference with a coverageData >= 2X There is a 2.15% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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% 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 43627872 0.17503616169526012 0.9046114638551275 chr2 243199373 45555339 0.18731684394597514 0.9322930469644504 chr3 198022430 36052718 0.18206380964015037 0.7628316922583914 chr4 191154276 33133814 0.17333545810923948 0.7759476835803811 chr5 180915260 32290260 0.178482788019098 0.7571486608681969 chr6 171115067 30218648 0.1765984055629654 0.8711380484127581 chr7 159138663 29566534 0.18579101673111328 1.2100963409812586 chr8 146364022 26223914 0.17916912668606497 0.9068856180759052 chr9 141213431 22348622 0.15826130589518783 0.7899880339487926 chr10 135534747 25176829 0.18575922084393606 0.8080434437276868 chr11 135006516 24164071 0.17898447953430632 1.1156789598827823 chr12 133851895 23743919 0.17738948708944316 0.7593854370903694 chr13 115169878 16501270 0.1432776545964562 0.6833975009006397 chr14 107349540 16156187 0.1505007566869872 0.7199898068041534 chr15 102531392 15739811 0.15351211656231098 0.7166483744097368 chr16 90354753 16196882 0.17925877125689227 0.8363444451107986 chr17 81195210 15353032 0.18908790309182033 0.8597073581609032 chr18 78077248 13483482 0.17269412466996786 0.9874965178281536 chr19 59128983 11313595 0.19133755437667513 0.9935212232847822 chr20 63025520 12135465 0.1925484311751811 0.8060250158479516 chr21 48129895 6824990 0.14180355057911512 0.7656797551729856 chr22 51304566 7019943 0.13682881558729101 0.7506118238961622 chrMT 16571 25865 1.5608593325689457 2.7777270244554835 chrX 155270560 15999773 0.10304447282214993 0.604057245541802 chrY 59373566 3278367 0.05521593565729234 0.45973272194326614