BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173971.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,545,830 number of mapped reads = 2,497,700 (98.11%) number of supplementary alignments = 320,862 (12.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,248,618 number of mapped paired reads (second in pair) = 1,249,082 number of mapped paired reads (both in pair) = 2,469,610 number of mapped paired reads (singletons) = 28,090 number of mapped bases = 279,609,063 bp number of sequenced bases = 279,410,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,940,348 duplication rate = 61.13% >>>>>>> Insert size mean insert size = 823,776.0643 std insert size = 8,322,982.694 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 52.5764 >>>>>>> ACTG content number of A's = 83,969,608 bp (30.05%) number of C's = 55,184,200 bp (19.75%) number of T's = 83,204,932 bp (29.78%) number of G's = 57,049,359 bp (20.42%) number of N's = 2,203 bp (0%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 2,297,326 number of insertions = 31,079 mapped reads with insertion percentage = 1.2% number of deletions = 84,031 mapped reads with deletion percentage = 3.28% homopolymer indels = 40.89% >>>>>>> Coverage mean coverageData = 0.0903X std coverageData = 1.7371X There is a 2.11% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 22780796 0.09139714841472751 1.0773126191166231 chr2 243199373 25876466 0.10640021674726932 5.159253891789812 chr3 198022430 19521437 0.09858194851967023 0.9485761976077021 chr4 191154276 18427124 0.09639922467651207 1.0833298663978195 chr5 180915260 18031454 0.09966795504149291 0.9556730080457908 chr6 171115067 16853057 0.09848961459366988 0.9965544802464819 chr7 159138663 15725732 0.09881779640187124 1.0932291100131188 chr8 146364022 14011656 0.0957315589482776 1.223136543979776 chr9 141213431 11694107 0.08281157760411614 1.0003932622769576 chr10 135534747 13705776 0.10112370667575009 1.3069577371048353 chr11 135006516 12637418 0.0936059856547961 0.9395471782673187 chr12 133851895 12429836 0.09286260758579473 0.9221481571514802 chr13 115169878 9269266 0.0804834229311244 0.8582372724834362 chr14 107349540 8419350 0.07842930673014528 0.8307382258053034 chr15 102531392 7552371 0.0736591092023797 0.8042377074889963 chr16 90354753 8309897 0.09196967203263784 1.0435719263549847 chr17 81195210 7707572 0.09492643716298042 0.9650625349445983 chr18 78077248 7863156 0.10070995330163277 1.2620808007774045 chr19 59128983 5239456 0.08861062264507408 0.9680743278224243 chr20 63025520 6200795 0.09838546353921396 0.9547430181777642 chr21 48129895 4015373 0.08342783627514666 0.9643805744398092 chr22 51304566 3325990 0.0648283429587924 0.8298750281754521 chrMT 16571 260396 15.713958119606541 19.37763935631284 chrX 155270560 7558313 0.0486783392808012 0.6655769292209971 chrY 59373566 2192269 0.03692331701956389 0.7037981710981114