BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004037.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 = 2,408,275 number of mapped reads = 2,173,064 (90.23%) number of supplementary alignments = 16,967 (0.7%) number of secondary alignments = 0 number of mapped bases = 147,032,587 bp number of sequenced bases = 146,965,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,794 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0742 >>>>>>> ACTG content number of A's = 41,444,786 bp (28.2%) number of C's = 27,729,080 bp (18.87%) number of T's = 45,398,780 bp (30.89%) number of G's = 32,279,487 bp (21.96%) number of N's = 113,759 bp (0.08%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,297,193 number of insertions = 11,514 mapped reads with insertion percentage = 0.52% number of deletions = 39,468 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.0475X std coverageData = 0.4016X There is a 4.04% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% 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 13822592 0.05545660004594331 0.7100917460120496 chr2 243199373 13062293 0.053710224820357574 0.47477988387662 chr3 198022430 4597843 0.023218799001709048 0.17298969226824099 chr4 191154276 7530271 0.039393683246719526 0.2400072243660471 chr5 180915260 6381455 0.035273171538984606 0.21473040033443713 chr6 171115067 8089469 0.047275024589155556 0.2727209371407153 chr7 159138663 5538661 0.0348039935461818 0.5442735757635748 chr8 146364022 13711120 0.09367821280560328 0.5640468716598048 chr9 141213431 5827357 0.04126630844342278 0.3871311561560984 chr10 135534747 8693689 0.06414361772483332 0.3903763688893739 chr11 135006516 4159501 0.030809631440307666 0.30214583130720074 chr12 133851895 8303889 0.062037888966756875 0.2835246930337914 chr13 115169878 3664088 0.031814638199061045 0.1992210757917066 chr14 107349540 4541372 0.04230453153315794 0.25142020231310136 chr15 102531392 5533414 0.05396799840579557 0.2706922079847971 chr16 90354753 5395376 0.05971325050271567 0.3388176221056241 chr17 81195210 4566655 0.05624291137371281 0.3036900768015808 chr18 78077248 3326422 0.0426042424036257 0.7396387312579884 chr19 59128983 2826796 0.04780728259777443 0.5032177464186192 chr20 63025520 2962235 0.04700056421589223 0.2544431513133559 chr21 48129895 2519774 0.0523536151491708 0.27326890594480824 chr22 51304566 2033590 0.03963760262585595 0.22376709934920036 chrMT 16571 6358 0.3836823366121538 0.7127969189472801 chrX 155270560 9557335 0.061552782446331104 0.3175299762352592 chrY 59373566 381032 0.006417536046260048 0.13083740567016752