BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716646.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 = 1,143,993 number of mapped reads = 1,020,407 (89.2%) number of supplementary alignments = 3,267 (0.29%) number of secondary alignments = 0 number of mapped bases = 58,400,281 bp number of sequenced bases = 58,380,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,227 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6356 >>>>>>> ACTG content number of A's = 15,114,251 bp (25.89%) number of C's = 10,625,624 bp (18.2%) number of T's = 18,199,261 bp (31.17%) number of G's = 14,440,467 bp (24.73%) number of N's = 1,174 bp (0%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 309,174 number of insertions = 4,675 mapped reads with insertion percentage = 0.46% number of deletions = 12,288 mapped reads with deletion percentage = 1.2% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.2034X There is a 1.76% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4966617 0.019926197094610246 0.33193840367434424 chr2 243199373 4625426 0.01901907041511986 0.2822722339874766 chr3 198022430 3415567 0.01724838443806593 0.1396246892168843 chr4 191154276 3740785 0.019569454988283913 0.16220278987865386 chr5 180915260 3444676 0.019040273330176792 0.1454286331598186 chr6 171115067 3152011 0.018420417647967844 0.16882236180743712 chr7 159138663 3303901 0.020761145894508365 0.25870323623446895 chr8 146364022 3044014 0.02079755638308436 0.2499453939704571 chr9 141213431 1941432 0.013748210678345462 0.14757543886744678 chr10 135534747 2565817 0.01893106422370051 0.20089466704648834 chr11 135006516 2089766 0.01547900102836518 0.15795155801944588 chr12 133851895 2893039 0.02161373210293362 0.1554689176090155 chr13 115169878 1810516 0.015720395223480222 0.13227369202490172 chr14 107349540 1973109 0.01838022780535436 0.14477799253372117 chr15 102531392 2124206 0.020717615927812627 0.15584693779602896 chr16 90354753 1834822 0.020306867531362738 0.15893936300179473 chr17 81195210 2464659 0.030354733979997096 0.18814769596189354 chr18 78077248 1115541 0.01428765778220052 0.22064002975512373 chr19 59128983 1436809 0.024299572343397146 0.26174239692716034 chr20 63025520 1839941 0.02919358697873496 0.18406218227367926 chr21 48129895 741329 0.015402672289228972 0.14424615242047092 chr22 51304566 496541 0.009678300368041317 0.10393194446119738 chrMT 16571 7687 0.46388268662120574 0.756247839825842 chrX 155270560 3164087 0.020377893916271057 0.15960227806622762 chrY 59373566 207983 0.00350295618087012 0.14598040464124268