BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124871.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 = 7,947,098 number of mapped reads = 7,730,582 (97.28%) number of supplementary alignments = 8,880 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,919,217 number of mapped paired reads (second in pair) = 3,811,365 number of mapped paired reads (both in pair) = 7,594,374 number of mapped paired reads (singletons) = 136,208 number of mapped bases = 481,411,126 bp number of sequenced bases = 481,215,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 507,294 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 30,216.2016 std insert size = 1,617,400.146 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 51.7883 >>>>>>> ACTG content number of A's = 133,093,796 bp (27.66%) number of C's = 85,417,274 bp (17.75%) number of T's = 145,015,832 bp (30.14%) number of G's = 117,685,295 bp (24.46%) number of N's = 3,627 bp (0%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 3,189,008 number of insertions = 49,935 mapped reads with insertion percentage = 0.64% number of deletions = 134,151 mapped reads with deletion percentage = 1.72% homopolymer indels = 48.44% >>>>>>> Coverage mean coverageData = 0.1555X std coverageData = 1.3331X There is a 11.61% of reference with a coverageData >= 1X There is a 2.45% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.2% 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 0.02% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 35382790 0.14195667741184886 1.4029272474343608 chr2 243199373 34638599 0.14242881703482024 1.2431182225986388 chr3 198022430 35217762 0.1778473377990564 0.5318117166823354 chr4 191154276 40862790 0.21376864203655063 0.8126136460981228 chr5 180915260 18032275 0.09967249307769836 0.38187572757609994 chr6 171115067 48748734 0.2848886124095665 2.493490994154659 chr7 159138663 10696866 0.06721726699438213 0.9011657410065101 chr8 146364022 44203425 0.30201018252969297 0.9776053105475863 chr9 141213431 24367969 0.17256127003953328 1.2354366237833492 chr10 135534747 29803550 0.2198960093975016 3.3856004985463612 chr11 135006516 27005369 0.2000301155834582 1.6417211464163624 chr12 133851895 25198705 0.1882581116987548 0.5494200908660785 chr13 115169878 23141251 0.20093145362192708 0.5571840111714764 chr14 107349540 7875472 0.07336288539289502 0.48877422408340515 chr15 102531392 5493559 0.05357928818522233 0.29610387637107904 chr16 90354753 9864540 0.10917566229194385 1.448310139925403 chr17 81195210 7983620 0.09832624362939636 1.3048052463984712 chr18 78077248 17236947 0.2207678605680364 1.8001886988103637 chr19 59128983 7181292 0.1214513024856186 1.2900029920486722 chr20 63025520 11916836 0.18907953476623438 0.5604747732925734 chr21 48129895 3461670 0.07192348954843969 0.47400826969210247 chr22 51304566 3748441 0.0730625223493753 0.32099074266936534 chrMT 16571 16573 1.0001206927765374 1.3606938352442766 chrX 155270560 8567220 0.055176074588769435 0.7935245601104686 chrY 59373566 764871 0.012882349023806318 0.5938244194798655