BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514701.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 59,394,214 number of mapped reads = 58,898,209 (99.16%) number of supplementary alignments = 5,804,135 (9.77%) number of secondary alignments = 0 number of mapped bases = 5,555,828,941 bp number of sequenced bases = 5,549,440,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,565,718 duplication rate = 48.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.3656 >>>>>>> ACTG content number of A's = 1,615,476,477 bp (29.11%) number of C's = 1,148,901,800 bp (20.7%) number of T's = 1,612,620,624 bp (29.06%) number of G's = 1,170,232,364 bp (21.09%) number of N's = 2,209,626 bp (0.04%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 43,328,854 number of insertions = 2,941,283 mapped reads with insertion percentage = 4.81% number of deletions = 2,346,628 mapped reads with deletion percentage = 3.74% homopolymer indels = 39.83% >>>>>>> Coverage mean coverageData = 1.7947X std coverageData = 291.3494X There is a 3.41% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 352534582 1.4143779485307681 87.40411966244987 chr2 243199373 318084813 1.3079178991139915 56.94187184100167 chr3 198022430 179938112 0.9086754061143477 58.06650846652249 chr4 191154276 339145041 1.774195420038629 146.4340885487011 chr5 180915260 280415127 1.5499805102123503 149.3364886201964 chr6 171115067 179570681 1.0494147835619876 58.72552293733121 chr7 159138663 275725993 1.732614738632057 84.06366104281301 chr8 146364022 265649370 1.8149909135456799 225.96575950800948 chr9 141213431 805081471 5.701167837215144 900.0189462126199 chr10 135534747 318401372 2.349223199568152 159.4610946234847 chr11 135006516 328899431 2.4361744954591673 195.69908051620254 chr12 133851895 228637291 1.7081363771502824 98.74340279217984 chr13 115169878 404108911 3.5088073202612926 939.5940513128212 chr14 107349540 157921471 1.4710959264473793 153.81765511129407 chr15 102531392 281086019 2.7414630145663095 297.9898991653137 chr16 90354753 144072210 1.594517224788385 103.82776309229818 chr17 81195210 125238245 1.5424339071233388 82.00602752328876 chr18 78077248 92569336 1.1856121773144463 63.36428281463628 chr19 59128983 137155710 2.3196020469352567 174.5099098035149 chr20 63025520 59550520 0.944863604457369 38.39230808298513 chr21 48129895 38948704 0.8092414080687274 34.8572686666833 chr22 51304566 39461235 0.7691563943840788 59.61369388912506 chrMT 16571 1614620 97.43648542634723 196.57479542150438 chrX 155270560 123826958 0.797491539928754 47.23081800498401 chrY 59373566 78191718 1.3169449515631249 49.48062004307328