BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818743.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 = 1,353,975 number of mapped reads = 1,319,047 (97.42%) number of supplementary alignments = 10,872 (0.8%) number of secondary alignments = 0 number of mapped bases = 89,610,689 bp number of sequenced bases = 89,573,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 558,419 duplication rate = 36.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7354 >>>>>>> ACTG content number of A's = 25,403,246 bp (28.36%) number of C's = 19,531,742 bp (21.81%) number of T's = 25,167,183 bp (28.1%) number of G's = 19,466,349 bp (21.73%) number of N's = 5,316 bp (0.01%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 440,983 number of insertions = 7,945 mapped reads with insertion percentage = 0.59% number of deletions = 22,724 mapped reads with deletion percentage = 1.71% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.371X There is a 1.45% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 7401818 0.029696287095709983 0.5205171074347167 chr2 243199373 7904464 0.03250199168893417 0.5432291855411628 chr3 198022430 6180992 0.03121359534876933 0.30977893385126226 chr4 191154276 5897288 0.03085093424747663 0.33687898885165696 chr5 180915260 5600807 0.03095817898390661 0.31643144034632703 chr6 171115067 5273266 0.03081707585691446 0.324353109748501 chr7 159138663 4832875 0.030368955657243395 0.3487070195350969 chr8 146364022 4712076 0.03219422324975464 0.34572831439266993 chr9 141213431 3781398 0.026777891969780126 0.31244287663290243 chr10 135534747 4293435 0.0316777438629815 0.38006386968773054 chr11 135006516 4208510 0.03117264354855287 0.3358312513594842 chr12 133851895 4184700 0.03126365898667329 0.3230439888372522 chr13 115169878 2825891 0.024536719575234768 0.27062912144264545 chr14 107349540 2812202 0.02619668421494866 0.29718799450326516 chr15 102531392 2584560 0.025207499377361425 0.2762657054882287 chr16 90354753 2679311 0.029653238053785617 0.391922338765687 chr17 81195210 2428643 0.029911161015532813 0.3158706880322907 chr18 78077248 2351324 0.030115354475608567 0.39053645234633905 chr19 59128983 1803846 0.03050696813100946 0.44787247883448 chr20 63025520 1903450 0.030201258157013224 0.317045434590067 chr21 48129895 1176683 0.024448069126267572 0.2925537967036835 chr22 51304566 1084291 0.021134395718307022 0.27797825895337125 chrMT 16571 180853 10.91382535755235 9.976411845262096 chrX 155270560 2684744 0.01729074719637773 0.23974508396485716 chrY 59373566 823262 0.013865800144124744 0.4492664592027514