BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231727.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,870,712 number of mapped reads = 4,555,533 (93.53%) number of supplementary alignments = 37,837 (0.78%) number of secondary alignments = 0 number of mapped bases = 311,461,213 bp number of sequenced bases = 311,351,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 493,490 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.262 >>>>>>> ACTG content number of A's = 82,830,225 bp (26.6%) number of C's = 56,852,812 bp (18.26%) number of T's = 90,175,604 bp (28.96%) number of G's = 81,426,010 bp (26.15%) number of N's = 66,490 bp (0.02%) GC percentage = 44.41% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,987,908 number of insertions = 20,413 mapped reads with insertion percentage = 0.44% number of deletions = 68,264 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.1006X std coverageData = 32.4908X There is a 6.51% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% 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 0.01% 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% 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 20609878 0.08268736871070825 0.8290216906529517 chr2 243199373 46008165 0.1891787977594827 115.89739319502094 chr3 198022430 22130655 0.11175832454939574 0.45663455782978546 chr4 191154276 21328919 0.11157960703949935 0.4754222497128111 chr5 180915260 13487175 0.07454968143649132 0.3751283429247213 chr6 171115067 17435900 0.10189576117221752 0.5157764100458356 chr7 159138663 19298795 0.12127031003144723 1.0269648494388606 chr8 146364022 14276005 0.09753766536970404 0.8440724230610588 chr9 141213431 10325342 0.07311869647866569 0.7521005810306068 chr10 135534747 15783317 0.1164521818157819 0.6432532853506017 chr11 135006516 10813910 0.08009917091705411 0.7643415863398676 chr12 133851895 13298267 0.0993506068778481 0.4468310233332188 chr13 115169878 8140031 0.07067847202199867 0.36271627960402497 chr14 107349540 8154509 0.07596221651252534 0.5239951479743532 chr15 102531392 9689611 0.09450384717297118 0.42399908586552415 chr16 90354753 8292584 0.09177806064059518 0.506184444499356 chr17 81195210 6841806 0.08426366530735002 0.48855224512255874 chr18 78077248 9470151 0.12129206961802752 1.6792660144338785 chr19 59128983 5222293 0.0883203589008118 0.7215547486001126 chr20 63025520 6292324 0.09983771653133525 0.4728269748895881 chr21 48129895 3655124 0.07594290409318366 0.4161588322666009 chr22 51304566 2675450 0.05214837993171992 0.30878467615779764 chrMT 16571 20574 1.2415665922394545 1.7616052932757935 chrX 155270560 17521874 0.11284736784616478 0.5674210765490545 chrY 59373566 688554 0.011596979032723082 0.19639102241373402