BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174011.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 = 5,710,968 number of mapped reads = 5,563,979 (97.43%) number of supplementary alignments = 545,055 (9.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,785,450 number of mapped paired reads (second in pair) = 2,778,529 number of mapped paired reads (both in pair) = 5,465,112 number of mapped paired reads (singletons) = 98,867 number of mapped bases = 654,505,850 bp number of sequenced bases = 654,137,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,373,976 duplication rate = 65.38% >>>>>>> Insert size mean insert size = 805,728.1936 std insert size = 8,151,201.8327 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.6553 >>>>>>> ACTG content number of A's = 197,409,640 bp (30.18%) number of C's = 127,966,482 bp (19.56%) number of T's = 196,796,755 bp (30.08%) number of G's = 131,957,048 bp (20.17%) number of N's = 7,579 bp (0%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 6,570,616 number of insertions = 70,243 mapped reads with insertion percentage = 1.21% number of deletions = 144,517 mapped reads with deletion percentage = 2.53% homopolymer indels = 42.77% >>>>>>> Coverage mean coverageData = 0.2114X std coverageData = 3.1936X There is a 4.19% of reference with a coverageData >= 1X There is a 3.33% of reference with a coverageData >= 2X There is a 2.61% of reference with a coverageData >= 3X There is a 2.17% of reference with a coverageData >= 4X There is a 1.68% of reference with a coverageData >= 5X There is a 1.38% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.86% of reference with a coverageData >= 8X There is a 0.64% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 57234141 0.2296248682164768 1.878218728508152 chr2 243199373 47217738 0.19415238377279861 9.141761409636942 chr3 198022430 40658810 0.2053242655390099 1.343619943054563 chr4 191154276 40690231 0.2128659209276595 1.9930450149606782 chr5 180915260 32160146 0.17776358942855347 1.235363417284019 chr6 171115067 30315316 0.1771633353595917 1.2940483246209744 chr7 159138663 59918321 0.3765164283176113 3.7956913892647925 chr8 146364022 63040655 0.43071141485849573 2.5911683024944026 chr9 141213431 22618506 0.16017248387655136 1.5183586570956793 chr10 135534747 30608379 0.22583418405613728 4.0884820674391635 chr11 135006516 28946332 0.21440692536647638 1.4114103971911056 chr12 133851895 24803255 0.1853037269289314 1.2744988055014894 chr13 115169878 17597696 0.1527977306705144 1.1679873991407497 chr14 107349540 22702368 0.21148081305238942 1.3647710689352681 chr15 102531392 15351944 0.14972920683647795 1.123040090167146 chr16 90354753 15554984 0.17215457387172536 1.7114356502791712 chr17 81195210 16073429 0.1979603107129103 1.486575888799946 chr18 78077248 11840760 0.15165442306573101 2.0956360991132157 chr19 59128983 8392128 0.14192917879206549 1.4304592155222098 chr20 63025520 25053644 0.39751586341532763 1.9107897432149636 chr21 48129895 7877782 0.16367752308622324 1.3143948236322922 chr22 51304566 8169596 0.1592372109726062 1.1108371277038434 chrMT 16571 1667942 100.65427554160884 72.39302981641636 chrX 155270560 24584952 0.15833621003234613 1.1828860499837959 chrY 59373566 1426795 0.024030811960999612 1.124604202014649