BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082963.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,076,038 number of mapped reads = 2,361,094 (76.76%) number of supplementary alignments = 15,425 (0.5%) number of secondary alignments = 0 number of mapped bases = 160,320,528 bp number of sequenced bases = 160,256,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,515 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8911 >>>>>>> ACTG content number of A's = 45,426,505 bp (28.35%) number of C's = 29,461,819 bp (18.38%) number of T's = 50,997,921 bp (31.82%) number of G's = 34,354,648 bp (21.44%) number of N's = 15,819 bp (0.01%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,532,491 number of insertions = 14,475 mapped reads with insertion percentage = 0.61% number of deletions = 36,695 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 0.0518X std coverageData = 0.466X There is a 4.4% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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% of reference with a coverageData >= 7X There is a 0% 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 13545039 0.05434305016235045 0.9802602036554612 chr2 243199373 13204733 0.054295917119819216 0.5018510692602077 chr3 198022430 9333468 0.04713338786924289 0.24894691440646732 chr4 191154276 10471255 0.05477907802596056 0.28380344557915516 chr5 180915260 9778307 0.05404910011460614 0.2664999634161027 chr6 171115067 11920748 0.06966509851525815 0.3774248050889595 chr7 159138663 9698522 0.06094384492849484 0.5417862471358297 chr8 146364022 8863322 0.06055669883135625 0.5163227581345795 chr9 141213431 6753468 0.04782454439478919 0.4426914778239814 chr10 135534747 6760192 0.049877925400192764 0.3998521313067099 chr11 135006516 8578644 0.06354244412914115 0.3959281015188838 chr12 133851895 8530568 0.06373139506168367 0.2926479737498882 chr13 115169878 3217649 0.02793828608553358 0.18930163594022928 chr14 107349540 4780037 0.04452778279254853 0.2644806116925241 chr15 102531392 3023129 0.029484911313795485 0.19471927199007716 chr16 90354753 3958017 0.04380529931834355 0.31069865306307143 chr17 81195210 5169443 0.06366684684970948 0.3554122531428415 chr18 78077248 4139722 0.053020849300426165 0.8532746025523926 chr19 59128983 2690311 0.04549902371904486 0.5986055638489368 chr20 63025520 3248130 0.051536742576657836 0.26351190848168776 chr21 48129895 2351945 0.048866613982847876 0.27896895225859736 chr22 51304566 1555236 0.030313793123208567 0.19509120848558262 chrMT 16571 37102 2.238971697543902 2.1115812005631143 chrX 155270560 8328751 0.05364024577485906 0.30017674840343395 chrY 59373566 382790 0.006447145182420069 0.1635447085499165