BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238536.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 = 3,331,031 number of mapped reads = 2,835,133 (85.11%) number of supplementary alignments = 31,073 (0.93%) number of secondary alignments = 0 number of mapped bases = 172,871,749 bp number of sequenced bases = 172,781,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,162,220 duplication rate = 20.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7418 >>>>>>> ACTG content number of A's = 43,588,492 bp (25.23%) number of C's = 30,094,947 bp (17.42%) number of T's = 58,694,375 bp (33.97%) number of G's = 40,399,355 bp (23.38%) number of N's = 3,972 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,055,197 number of insertions = 10,027 mapped reads with insertion percentage = 0.35% number of deletions = 54,674 mapped reads with deletion percentage = 1.91% homopolymer indels = 41.42% >>>>>>> Coverage mean coverageData = 0.0558X std coverageData = 1.1312X There is a 1.44% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 21465756 0.08612117359579216 1.6439017998215537 chr2 243199373 19769030 0.08128733950313269 2.2485669899932774 chr3 198022430 9281657 0.04687174579162573 0.6605092542411499 chr4 191154276 7995770 0.04182888380692044 0.5909983120717395 chr5 180915260 7061108 0.03902991931139474 0.5924295943915082 chr6 171115067 17736373 0.10365173161519435 1.1857951984062085 chr7 159138663 9994747 0.06280527190303213 0.8273995572216282 chr8 146364022 9032213 0.06171060945564887 0.8679858514221951 chr9 141213431 5000260 0.03540923809152403 0.5535763293071726 chr10 135534747 5847567 0.043144412259093975 0.8242142158266452 chr11 135006516 7312007 0.05416040067280901 0.7458365616355954 chr12 133851895 9664507 0.07220298972980548 0.8078936323604282 chr13 115169878 3095596 0.02687852113553511 0.7699910422496731 chr14 107349540 7321694 0.06820424195576431 0.7903935779686916 chr15 102531392 6531754 0.06370491878233742 0.8399349698903623 chr16 90354753 3425838 0.03791541547349479 0.5822020609014972 chr17 81195210 2677001 0.032969937512323695 0.5269645743100514 chr18 78077248 6811583 0.08724158669117026 2.889950266304046 chr19 59128983 3161263 0.053463848684831936 1.1989299251498224 chr20 63025520 1738296 0.0275808275758772 0.46329191093442296 chr21 48129895 1629538 0.03385708612079873 0.5332353530494349 chr22 51304566 870100 0.01695950415017642 0.34934894068647276 chrMT 16571 168624 10.17584937541488 11.271390353516153 chrX 155270560 4911655 0.03163288005144053 0.5085101462168874 chrY 59373566 367812 0.006194878037138615 0.34196989304091