BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236083.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 = 2,364,136 number of mapped reads = 2,054,821 (86.92%) number of supplementary alignments = 11,553 (0.49%) number of secondary alignments = 0 number of mapped bases = 134,442,999 bp number of sequenced bases = 134,368,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,462 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6275 >>>>>>> ACTG content number of A's = 36,659,013 bp (27.28%) number of C's = 23,999,465 bp (17.86%) number of T's = 43,302,591 bp (32.23%) number of G's = 30,352,954 bp (22.59%) number of N's = 54,224 bp (0.04%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,093,638 number of insertions = 9,953 mapped reads with insertion percentage = 0.48% number of deletions = 43,048 mapped reads with deletion percentage = 2.07% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.4748X There is a 3.61% of reference with a coverageData >= 1X There is a 0.52% 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 16930287 0.06792475353551877 0.9464822732813326 chr2 243199373 4932917 0.020283428115581533 0.40608421077266926 chr3 198022430 11335737 0.05724471212680301 0.27617630436058954 chr4 191154276 5420132 0.02835475153064324 0.2471154552751775 chr5 180915260 7661362 0.042347793104904476 0.24179342071383342 chr6 171115067 14063239 0.08218586034858053 0.5461098720603973 chr7 159138663 11324600 0.07116183953361478 0.694628977353912 chr8 146364022 7584820 0.05182161501410504 0.8385749496443251 chr9 141213431 4467701 0.03163793251365729 0.3743603300388322 chr10 135534747 2723913 0.020097525249373874 0.36300822338660677 chr11 135006516 4346264 0.03219299429962329 0.2917962136034533 chr12 133851895 4373901 0.032677169045682915 0.21849287127344486 chr13 115169878 4776327 0.04147201579913109 0.23328528210278957 chr14 107349540 2863033 0.026670193463334824 0.2158092720215926 chr15 102531392 5786797 0.05643927081376209 0.2792457308058354 chr16 90354753 3377516 0.03738061239567552 0.2607466167641903 chr17 81195210 3620941 0.044595500153272585 0.2922383713227247 chr18 78077248 4412773 0.056518039672709776 0.6979515568495245 chr19 59128983 3300654 0.055821254358459034 0.5684774579802632 chr20 63025520 2017042 0.03200357569441712 0.21760007342025095 chr21 48129895 1895061 0.039373886022398344 0.26589767102440715 chr22 51304566 1462849 0.028513037221677306 0.19136494375170296 chrMT 16571 74678 4.5065475831271495 3.602515508175714 chrX 155270560 5356902 0.03450043588430415 0.24563946384982738 chrY 59373566 333553 0.005617870417283005 0.19154400026924903