BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117302.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 1,144,147 number of mapped reads = 1,105,281 (96.6%) number of supplementary alignments = 8,157 (0.71%) number of secondary alignments = 0 number of mapped bases = 255,673,203 bp number of sequenced bases = 255,179,085 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 347,296 duplication rate = 24.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 53.5704 >>>>>>> ACTG content number of A's = 72,033,366 bp (28.23%) number of C's = 55,170,106 bp (21.62%) number of T's = 73,953,349 bp (28.98%) number of G's = 54,022,264 bp (21.17%) number of N's = 0 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,371,615 number of insertions = 1,237,972 mapped reads with insertion percentage = 49.26% number of deletions = 397,100 mapped reads with deletion percentage = 25.31% homopolymer indels = 29.97% >>>>>>> Coverage mean coverageData = 0.0826X std coverageData = 1.1745X There is a 5.14% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% 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 0.01% 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 22189132 0.08902337699692231 3.4678866205468895 chr2 243199373 21501631 0.08841153961363214 0.47075342212758076 chr3 198022430 17505602 0.08840211687130595 0.44812242498045407 chr4 191154276 16389338 0.08573879874913183 0.5271521739158115 chr5 180915260 15662469 0.08657350960886329 0.4435596843213567 chr6 171115067 15293399 0.08937494089868778 0.4549699438542218 chr7 159138663 14024518 0.08812766008974199 1.9046035696035175 chr8 146364022 13073711 0.08932325595698648 0.4784285415104268 chr9 141213431 10897186 0.07716819797402982 0.44924575612652456 chr10 135534747 12280073 0.09060461078663466 0.6563019694388094 chr11 135006516 11386053 0.08433706266444206 0.43739661207469943 chr12 133851895 11541857 0.08622856628215834 0.44538253365087066 chr13 115169878 8312885 0.07217933321072026 0.4059289389952758 chr14 107349540 7663556 0.0713888107950905 0.40467603524044904 chr15 102531392 7614639 0.0742664158894868 0.41771154535732774 chr16 90354753 7092602 0.07849727617538836 0.5941083478325406 chr17 81195210 6416723 0.0790283441597109 0.53863263358526 chr18 78077248 7015530 0.08985370488468036 0.5263893724351755 chr19 59128983 4072200 0.06886977914029065 1.249397388148138 chr20 63025520 5538480 0.0878767838805614 0.5326399310901576 chr21 48129895 3367735 0.06997179196006972 0.5313977427443709 chr22 51304566 2790348 0.054387907696168795 0.3679000835601265 chrMT 16571 17924 1.0816486633274998 3.7650984515719403 chrX 155270560 13644249 0.08787402454141983 0.4590466476213632 chrY 59373566 381363 0.006423110917744102 0.40179398826313545