BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068059.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 = 1,716,534 number of mapped reads = 1,322,116 (77.02%) number of supplementary alignments = 13,437 (0.78%) number of secondary alignments = 0 number of mapped bases = 85,033,522 bp number of sequenced bases = 85,001,164 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,883 duplication rate = 13.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6744 >>>>>>> ACTG content number of A's = 22,835,714 bp (26.87%) number of C's = 15,030,913 bp (17.68%) number of T's = 27,602,685 bp (32.47%) number of G's = 19,442,176 bp (22.87%) number of N's = 89,676 bp (0.11%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 739,950 number of insertions = 6,390 mapped reads with insertion percentage = 0.48% number of deletions = 19,914 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.4024X There is a 1.18% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 7192467 0.028856365417039422 0.5624118491362704 chr2 243199373 6710639 0.02759315913203444 0.4550365923421671 chr3 198022430 5497452 0.027761764159746953 0.3415354760738004 chr4 191154276 5858780 0.03064948439866446 0.3696427881577035 chr5 180915260 5102722 0.028205039199015052 0.3449453551092598 chr6 171115067 5113451 0.029883113682794515 0.3771249624009666 chr7 159138663 5386159 0.03384569719553318 0.6390927975727028 chr8 146364022 3867182 0.026421670757312204 0.3689260577758265 chr9 141213431 3396564 0.024052697933527302 0.34992408780758566 chr10 135534747 4326016 0.03191813240334598 0.41319588032414817 chr11 135006516 3642283 0.02697857190833663 0.3471625257979566 chr12 133851895 3666689 0.027393627860106125 0.33407955379062537 chr13 115169878 2460663 0.021365508436155502 0.29824613023475444 chr14 107349540 2615186 0.02436140853514603 0.3261834352307553 chr15 102531392 2284270 0.022278737813293318 0.3147603807688593 chr16 90354753 2366031 0.02618601591440353 0.3230729528429661 chr17 81195210 2421853 0.029827535392789796 0.35095930685818516 chr18 78077248 2128500 0.027261462904020387 0.4684127544542403 chr19 59128983 1754804 0.029677561002528996 0.44692346421015133 chr20 63025520 1605787 0.025478361781069003 0.3204860405354134 chr21 48129895 1182528 0.024569511319316197 0.3195414598268628 chr22 51304566 877414 0.017102064560881383 0.24837027871014103 chrMT 16571 118291 7.138434614688311 6.364967144752722 chrX 155270560 5213220 0.03357507050918088 0.386468194100434 chrY 59373566 244571 0.004119190011258545 0.13159134567623545