BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819088.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,344,454 number of mapped reads = 1,195,444 (88.92%) number of supplementary alignments = 6,246 (0.46%) number of secondary alignments = 0 number of mapped bases = 68,398,725 bp number of sequenced bases = 68,355,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,866 duplication rate = 5.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2741 >>>>>>> ACTG content number of A's = 16,759,554 bp (24.52%) number of C's = 12,137,648 bp (17.76%) number of T's = 21,497,404 bp (31.45%) number of G's = 17,959,752 bp (26.27%) number of N's = 886 bp (0%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 446,683 number of insertions = 4,308 mapped reads with insertion percentage = 0.36% number of deletions = 25,512 mapped reads with deletion percentage = 2.11% homopolymer indels = 41.5% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2395X There is a 1.79% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.06% 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% 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 6744386 0.027058652744540203 0.37006852849430494 chr2 243199373 5039086 0.02071997940553901 0.31582186565409903 chr3 198022430 3800352 0.019191522899703838 0.16656858782510256 chr4 191154276 4548576 0.023795313896090926 0.22082099654862303 chr5 180915260 4332432 0.023947299967951845 0.18640942173227884 chr6 171115067 3047871 0.017811821328393016 0.18083275791242384 chr7 159138663 3274206 0.020574547619518456 0.278869117836253 chr8 146364022 5998479 0.04098328891235307 0.27814390999188227 chr9 141213431 3129234 0.022159606050503794 0.23558376002382922 chr10 135534747 3126239 0.02306595960960476 0.25582712554324377 chr11 135006516 2049131 0.015178015555930648 0.22033933244761014 chr12 133851895 2726646 0.02037061933265868 0.1722429902347211 chr13 115169878 1564891 0.013587676110935882 0.1388564150141375 chr14 107349540 1661625 0.01547864108220678 0.14960560496892295 chr15 102531392 1891366 0.018446701669670103 0.16435706830673663 chr16 90354753 2326988 0.025753908042889566 0.20217263736319419 chr17 81195210 2021816 0.024900680717495526 0.20019288989804798 chr18 78077248 1598399 0.02047202022284392 0.325880809912177 chr19 59128983 1265674 0.021405306429843382 0.25578411126214606 chr20 63025520 2057781 0.0326499646492405 0.22320722569322848 chr21 48129895 778329 0.016171425264900327 0.17820853660241273 chr22 51304566 587937 0.011459740250019852 0.12951601752178968 chrMT 16571 22356 1.3491038561342104 1.4419240429158455 chrX 155270560 4536883 0.029219209359456166 0.22132967563592598 chrY 59373566 268042 0.0045145006112652895 0.17123627381405343