BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524432.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 = 388,625 number of mapped reads = 354,216 (91.15%) number of supplementary alignments = 1,530 (0.39%) number of secondary alignments = 0 number of mapped bases = 20,698,254 bp number of sequenced bases = 20,692,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,329 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4915 >>>>>>> ACTG content number of A's = 5,176,201 bp (25.01%) number of C's = 3,983,631 bp (19.25%) number of T's = 6,572,914 bp (31.76%) number of G's = 4,957,568 bp (23.96%) number of N's = 2,213 bp (0.01%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 105,308 number of insertions = 1,554 mapped reads with insertion percentage = 0.44% number of deletions = 3,550 mapped reads with deletion percentage = 0.99% homopolymer indels = 39.03% >>>>>>> Coverage mean coverageData = 0.0067X std coverageData = 0.0995X There is a 0.63% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1689618 0.006778791536090094 0.15020378874252494 chr2 243199373 1716478 0.007057904709318473 0.12102821762494494 chr3 198022430 1431367 0.0072283074195180815 0.08805665208303115 chr4 191154276 1366832 0.007150412894765692 0.0936485712146727 chr5 180915260 1274895 0.00704691798801273 0.086894944397354 chr6 171115067 802893 0.004692123341774456 0.07350664958652103 chr7 159138663 1178930 0.0074081934444805535 0.11657878938547844 chr8 146364022 1071719 0.0073222844340803915 0.092249320480867 chr9 141213431 781652 0.005535252521412074 0.08030568368484735 chr10 135534747 1048511 0.007736104749581301 0.10389278317652098 chr11 135006516 846877 0.006272860192910985 0.08680650130203742 chr12 133851895 951617 0.007109477232279752 0.08736659707737986 chr13 115169878 665828 0.005781268605667881 0.07843150536354355 chr14 107349540 554379 0.005164241970668901 0.07460107290142225 chr15 102531392 635840 0.006201417805777962 0.08138444741442796 chr16 90354753 629940 0.006971852382796066 0.08765407316629026 chr17 81195210 569526 0.0070142807685330206 0.08831157277257955 chr18 78077248 546660 0.007001527512854961 0.10495319257744622 chr19 59128983 601339 0.010169953371259574 0.13610990090842467 chr20 63025520 584056 0.009266976297855218 0.10070716209097998 chr21 48129895 287920 0.005982144777170197 0.08575295649002966 chr22 51304566 154018 0.0030020329964393425 0.0566326514270616 chrMT 16571 40655 2.4533824150624586 2.389706871969323 chrX 155270560 1193976 0.007689648314529168 0.09274313660552484 chrY 59373566 72728 0.0012249222153845366 0.05144461017274711