BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008824.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 = 2,254,809 number of mapped reads = 1,562,130 (69.28%) number of supplementary alignments = 10,016 (0.44%) number of secondary alignments = 0 number of mapped bases = 102,893,361 bp number of sequenced bases = 102,842,569 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,821 duplication rate = 4.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7066 >>>>>>> ACTG content number of A's = 27,652,209 bp (26.89%) number of C's = 20,002,154 bp (19.45%) number of T's = 31,502,530 bp (30.63%) number of G's = 23,532,163 bp (22.88%) number of N's = 153,513 bp (0.15%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 887,002 number of insertions = 7,887 mapped reads with insertion percentage = 0.5% number of deletions = 27,898 mapped reads with deletion percentage = 1.76% homopolymer indels = 44.98% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.3315X There is a 2.58% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 9493771 0.038089257157758495 0.4189455668140202 chr2 243199373 7971489 0.032777588616562756 0.40393069202793913 chr3 198022430 5815540 0.029368087241430176 0.21630049847429283 chr4 191154276 9045553 0.04732069399274123 0.31025071997901954 chr5 180915260 4799143 0.02652702154588839 0.20012951267162357 chr6 171115067 5624072 0.03286719339565814 0.2522881630382848 chr7 159138663 7392217 0.04645142079646603 0.45057194131937084 chr8 146364022 6353286 0.043407429730237944 0.4727947479428944 chr9 141213431 5485334 0.03884427962096608 0.35522044607138464 chr10 135534747 5144385 0.03795620764319573 0.4559084035951024 chr11 135006516 3741148 0.02771086989608709 0.2769334057995505 chr12 133851895 2413325 0.018029815715347175 0.1791609005673504 chr13 115169878 2996981 0.0260222642590626 0.19770058890195372 chr14 107349540 3793301 0.03533597815137354 0.27470064431549335 chr15 102531392 3810450 0.037163740057288994 0.23865236442042007 chr16 90354753 2439352 0.026997495084735607 0.290940084637085 chr17 81195210 3803507 0.04684398254527576 0.3019985526553965 chr18 78077248 3041982 0.03896118367286716 0.5773821580350927 chr19 59128983 897129 0.015172407074885763 0.3001428526274802 chr20 63025520 2140621 0.03396435285262224 0.24019985551293432 chr21 48129895 1064957 0.02212672601924438 0.24496884514776188 chr22 51304566 1905030 0.03713178277348648 0.2401166283473466 chrMT 16571 6496 0.39201013819322916 0.699777899686153 chrX 155270560 3350861 0.021580787755257663 0.20660721117793926 chrY 59373566 363431 0.006121090991907072 0.2602016991681158