BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525030.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 = 778,537 number of mapped reads = 677,246 (86.99%) number of supplementary alignments = 5,461 (0.7%) number of secondary alignments = 0 number of mapped bases = 38,641,781 bp number of sequenced bases = 38,631,005 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,273 duplication rate = 1.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1511 >>>>>>> ACTG content number of A's = 9,141,557 bp (23.66%) number of C's = 7,113,963 bp (18.42%) number of T's = 12,431,164 bp (32.18%) number of G's = 9,943,970 bp (25.74%) number of N's = 351 bp (0%) GC percentage = 44.16% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 189,458 number of insertions = 2,739 mapped reads with insertion percentage = 0.4% number of deletions = 6,477 mapped reads with deletion percentage = 0.95% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.0125X std coverageData = 0.1638X There is a 1.18% of reference with a coverageData >= 1X There is a 0.03% 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 3092950 0.01240899616454717 0.3086649585546665 chr2 243199373 3227688 0.013271777637354354 0.16857487614790495 chr3 198022430 2535320 0.012803196082383193 0.11830817190886427 chr4 191154276 2434137 0.012733887260779874 0.12570769914081822 chr5 180915260 2303433 0.012732110049754785 0.11788802896010077 chr6 171115067 2215028 0.01294466956553861 0.13978078825452614 chr7 159138663 2147507 0.013494564799755795 0.1991313499925024 chr8 146364022 1971093 0.013467059548281613 0.1564950942328832 chr9 141213431 1609627 0.011398540412207675 0.13927755343518133 chr10 135534747 1887538 0.013926598468509334 0.17407633958372856 chr11 135006516 1774167 0.013141343488932046 0.15389587654199316 chr12 133851895 1754990 0.013111431855335332 0.11946661541144084 chr13 115169878 1191683 0.01034717602114678 0.10441045193932587 chr14 107349540 1176695 0.010961341799881024 0.11241199904565298 chr15 102531392 1105478 0.010781849133580474 0.11630491795727764 chr16 90354753 1152454 0.012754768971589132 0.12629667325754068 chr17 81195210 1071380 0.013195113357056408 0.1299895194011528 chr18 78077248 1016749 0.013022346791731185 0.23003280912467453 chr19 59128983 860273 0.014549091771120095 0.21349121392027143 chr20 63025520 807594 0.012813761790462022 0.1182738054228939 chr21 48129895 498183 0.010350801721050918 0.11135746579194146 chr22 51304566 459950 0.008965088994223243 0.09691950860922352 chrMT 16571 5418 0.32695673163961136 0.6588045499260846 chrX 155270560 2196020 0.01414318335684498 0.13608084181651853 chrY 59373566 146426 0.002466181667444398 0.08426529320753967