BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013166.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 = 1,408,335 number of mapped reads = 906,501 (64.37%) number of supplementary alignments = 6,897 (0.49%) number of secondary alignments = 0 number of mapped bases = 54,769,229 bp number of sequenced bases = 54,714,465 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,822 duplication rate = 17.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4846 >>>>>>> ACTG content number of A's = 14,801,772 bp (27.05%) number of C's = 9,584,596 bp (17.52%) number of T's = 17,831,712 bp (32.59%) number of G's = 12,416,056 bp (22.69%) number of N's = 80,329 bp (0.15%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 630,497 number of insertions = 3,793 mapped reads with insertion percentage = 0.42% number of deletions = 31,965 mapped reads with deletion percentage = 3.45% homopolymer indels = 40.44% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 0.3603X There is a 0.65% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 2978473 0.011949711451270566 0.3022819837411878 chr2 243199373 4342046 0.017853853595255775 0.4296669838235628 chr3 198022430 4185985 0.021138943704508625 0.3607824187420567 chr4 191154276 5463328 0.02858072607279787 0.4213075811245301 chr5 180915260 2039184 0.01127148699341338 0.27662825324803575 chr6 171115067 1979232 0.011566672851783415 0.2870431429403215 chr7 159138663 6885712 0.04326863045217365 0.6003006447312331 chr8 146364022 3118447 0.02130610349037826 0.4651958227695359 chr9 141213431 1505878 0.010663844007869195 0.2647000964817055 chr10 135534747 1888926 0.01393683938481104 0.30184958775363196 chr11 135006516 2583669 0.019137365192062286 0.3488318973210928 chr12 133851895 1693515 0.012652155578372648 0.27372997007591465 chr13 115169878 806247 0.00700050233620982 0.2174081062155485 chr14 107349540 1481983 0.013805210530012518 0.30069836595765365 chr15 102531392 1743838 0.01700784477791933 0.3263488139119255 chr16 90354753 1378904 0.015261001266861966 0.33246066577296074 chr17 81195210 1137552 0.014010087540878334 0.2870735268933841 chr18 78077248 1355809 0.01736496911366548 0.44633779137355634 chr19 59128983 904888 0.015303628679018544 0.32499315074468205 chr20 63025520 1708435 0.02710703537233806 0.4111320473030485 chr21 48129895 688239 0.014299615654677826 0.28805566308295216 chr22 51304566 381281 0.00743171670139457 0.23613899654990825 chrMT 16571 37565 2.2669120753122924 3.7304987661063103 chrX 155270560 4265190 0.027469405661961932 0.40477109203539713 chrY 59373566 214903 0.0036195063641621256 0.12228613861539114