BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524323.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,136,437 number of mapped reads = 2,862,743 (91.27%) number of supplementary alignments = 11,643 (0.37%) number of secondary alignments = 0 number of mapped bases = 165,682,009 bp number of sequenced bases = 165,638,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,741 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6905 >>>>>>> ACTG content number of A's = 39,866,993 bp (24.07%) number of C's = 31,394,591 bp (18.95%) number of T's = 52,821,506 bp (31.89%) number of G's = 41,532,074 bp (25.07%) number of N's = 23,149 bp (0.01%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 841,726 number of insertions = 10,606 mapped reads with insertion percentage = 0.37% number of deletions = 26,960 mapped reads with deletion percentage = 0.94% homopolymer indels = 42.58% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.4434X There is a 4.55% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 13967020 0.05603604895331434 0.8327613956322111 chr2 243199373 10719192 0.044075738632763664 0.6386249942816165 chr3 198022430 11505718 0.05810310478464485 0.2770743199274182 chr4 191154276 8501695 0.04447556799618754 0.2933190286692064 chr5 180915260 9652227 0.05335219925616004 0.26579416985645277 chr6 171115067 10621892 0.06207455711658635 0.31820585056732 chr7 159138663 7524406 0.04728207374722006 0.5324962962078665 chr8 146364022 17089216 0.11675831100077312 0.5343540583759467 chr9 141213431 6857246 0.04855944616202973 0.3335362819719046 chr10 135534747 8474800 0.06252861489459968 0.44646952094700665 chr11 135006516 7940626 0.05881661296999917 0.3632143959754425 chr12 133851895 6531678 0.0487977999863207 0.25915943457014584 chr13 115169878 4137129 0.0359219708472731 0.216533270808922 chr14 107349540 3424757 0.031902856779824115 0.21964944157326993 chr15 102531392 5129106 0.05002473778957375 0.2641122567397011 chr16 90354753 5318550 0.0588629797925517 0.30236086267985346 chr17 81195210 5233170 0.06445170841974546 0.3281164836023887 chr18 78077248 3796006 0.04861859372912324 0.6028294195935641 chr19 59128983 2999635 0.05073036686594119 0.5646332059521152 chr20 63025520 3845431 0.061013871841120865 0.29728863396451716 chr21 48129895 2404341 0.04995525130482832 0.293169122283417 chr22 51304566 1261425 0.024586992900397987 0.18001681999133926 chrMT 16571 300695 18.145857220445357 10.972500494193449 chrX 155270560 7976347 0.05137063329970601 0.3013296619820654 chrY 59373566 469701 0.007910944746017109 0.2131898365805467