BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524351.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,441,246 number of mapped reads = 1,328,745 (92.19%) number of supplementary alignments = 6,618 (0.46%) number of secondary alignments = 0 number of mapped bases = 78,413,227 bp number of sequenced bases = 78,390,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,736 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2723 >>>>>>> ACTG content number of A's = 18,802,250 bp (23.99%) number of C's = 14,443,327 bp (18.42%) number of T's = 25,440,287 bp (32.45%) number of G's = 19,694,494 bp (25.12%) number of N's = 10,537 bp (0.01%) GC percentage = 43.55% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 403,353 number of insertions = 4,795 mapped reads with insertion percentage = 0.36% number of deletions = 13,801 mapped reads with deletion percentage = 1.03% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.2771X There is a 2.24% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6103137 0.024485945011948437 0.4925299088763958 chr2 243199373 6567976 0.027006549889419328 0.3273433078831438 chr3 198022430 5070742 0.025606907257930328 0.1755008485463438 chr4 191154276 5898799 0.030858838857468197 0.226440726869738 chr5 180915260 4541437 0.0251025645929481 0.1762357013867458 chr6 171115067 4304884 0.025157831367357032 0.18443779698617946 chr7 159138663 4662956 0.02930121387283491 0.38678464781178035 chr8 146364022 3918507 0.026772337535244828 0.23875946186120456 chr9 141213431 3216419 0.022777004830369145 0.2176859179649195 chr10 135534747 3732614 0.027539904582549596 0.2700959731478125 chr11 135006516 3512720 0.026018892302946326 0.22903106731826958 chr12 133851895 3409709 0.025473744693715394 0.17796871219040103 chr13 115169878 2273220 0.019737973500327924 0.1546234828671219 chr14 107349540 2305983 0.02148107015642545 0.16753093274224276 chr15 102531392 2214849 0.021601667126493317 0.15992903842395848 chr16 90354753 2246806 0.024866494848367303 0.18414589001939935 chr17 81195210 2178143 0.026826003652185886 0.1909040576637292 chr18 78077248 2005686 0.025688482257981225 0.42715007798139054 chr19 59128983 1644978 0.027820163928745402 0.3404314080670845 chr20 63025520 1675052 0.026577361043589962 0.1839081265583149 chr21 48129895 1039006 0.02158753930379445 0.19256182319723947 chr22 51304566 962067 0.018752073645842752 0.15088409862595553 chrMT 16571 434625 26.228049001267273 15.726534250494414 chrX 155270560 4211189 0.02712161919168708 0.19924975599844064 chrY 59373566 281723 0.004744923018435511 0.15697264153191043