BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525182.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 = 1,869,803 number of mapped reads = 1,657,319 (88.64%) number of supplementary alignments = 6,952 (0.37%) number of secondary alignments = 0 number of mapped bases = 94,682,618 bp number of sequenced bases = 94,658,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,071 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3424 >>>>>>> ACTG content number of A's = 25,223,868 bp (26.65%) number of C's = 17,136,368 bp (18.1%) number of T's = 29,338,636 bp (30.99%) number of G's = 22,956,549 bp (24.25%) number of N's = 2,693 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 454,032 number of insertions = 6,021 mapped reads with insertion percentage = 0.36% number of deletions = 14,737 mapped reads with deletion percentage = 0.88% homopolymer indels = 41.46% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.2646X There is a 2.74% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7537243 0.030239615731990493 0.45353284889196493 chr2 243199373 8134632 0.03344840860259948 0.29041015939478176 chr3 198022430 6390402 0.03227110181407227 0.1958020237258868 chr4 191154276 6214863 0.03251228866049536 0.2184517157649997 chr5 180915260 5714334 0.03158569376624172 0.19526329525550767 chr6 171115067 5456687 0.031888991984557385 0.2129267041614064 chr7 159138663 5178205 0.032538950009904255 0.29841046312577413 chr8 146364022 4779677 0.03265609221916572 0.277256770471825 chr9 141213431 4013831 0.02842386146683172 0.2573226338191052 chr10 135534747 4495775 0.033170645163044424 0.27503984765300643 chr11 135006516 4279042 0.03169507759166232 0.25839041757418707 chr12 133851895 4270272 0.03190296259907265 0.20066535027513363 chr13 115169878 3011580 0.026149024834427628 0.1750818901204847 chr14 107349540 2874760 0.026779434732556843 0.19580256881577088 chr15 102531392 2690278 0.026238578717433195 0.17732444088082502 chr16 90354753 2711165 0.030005781765570207 0.2013660381765845 chr17 81195210 2489851 0.030664998587970893 0.20349404395990106 chr18 78077248 2556933 0.032748759280040195 0.43743334284943836 chr19 59128983 1827896 0.030913706058499264 0.3298053930085389 chr20 63025520 1989634 0.031568704232825054 0.2000172826292387 chr21 48129895 1252531 0.026023971172178955 0.1968310997915344 chr22 51304566 1076807 0.020988521762371013 0.1576743133874967 chrMT 16571 13657 0.8241506245851186 1.0875657937819585 chrX 155270560 5438651 0.035026929766982226 0.23034470243403732 chrY 59373566 283912 0.004781791277283227 0.12119541933874965