BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173878.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 = 1,857,730 number of mapped reads = 1,818,510 (97.89%) number of supplementary alignments = 197,641 (10.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 907,669 number of mapped paired reads (second in pair) = 910,841 number of mapped paired reads (both in pair) = 1,793,680 number of mapped paired reads (singletons) = 24,830 number of mapped bases = 216,176,662 bp number of sequenced bases = 216,064,905 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,426,003 duplication rate = 64.58% >>>>>>> Insert size mean insert size = 848,737.5275 std insert size = 8,507,841.6868 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.5917 >>>>>>> ACTG content number of A's = 65,534,748 bp (30.33%) number of C's = 41,929,385 bp (19.41%) number of T's = 65,366,733 bp (30.25%) number of G's = 43,231,466 bp (20.01%) number of N's = 2,573 bp (0%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 2,128,661 number of insertions = 23,567 mapped reads with insertion percentage = 1.25% number of deletions = 40,618 mapped reads with deletion percentage = 2.16% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 0.0698X std coverageData = 1.1772X There is a 1.49% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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% 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 18858191 0.0756595547258436 0.9759041647263541 chr2 243199373 22617627 0.09300035078626621 2.993013064318174 chr3 198022430 16656672 0.08411507726675205 0.8532343275055572 chr4 191154276 13298267 0.06956824235519586 0.834543113696575 chr5 180915260 13670566 0.0755633659648169 0.8060646410033491 chr6 171115067 12086387 0.07063309626615172 0.7927380134846305 chr7 159138663 14256668 0.08958645077972033 1.2114217174070059 chr8 146364022 9120863 0.0623162910896231 0.8384186791911444 chr9 141213431 8855665 0.06271120910588172 0.8025354222038472 chr10 135534747 8679569 0.0640394377981906 1.157876634718144 chr11 135006516 10527237 0.07797576970284902 0.8164875809677805 chr12 133851895 8472245 0.0632956671999302 0.7332266181934448 chr13 115169878 7589603 0.06589920152559335 0.7633230154603443 chr14 107349540 5143846 0.047916795917336955 0.6350652000923519 chr15 102531392 5274146 0.05143932894230091 0.6520892372819934 chr16 90354753 8417708 0.09316286880890483 1.047911578166051 chr17 81195210 4864905 0.059916157615701716 0.7498135246295549 chr18 78077248 3628842 0.046477585890322366 0.8926661523813398 chr19 59128983 4713604 0.07971731900073438 0.992962311968381 chr20 63025520 6344092 0.10065909809232831 0.9132627711569058 chr21 48129895 3249729 0.0675199686182569 0.7763155230805335 chr22 51304566 2011183 0.03920085787296203 0.5434416533647567 chrMT 16571 376557 22.723854927282602 21.98640059852369 chrX 155270560 7154453 0.046077331079375256 0.6255712432055283 chrY 59373566 308037 0.005188116880161788 0.3193298381721756