BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524864.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 = 1,814,849 number of mapped reads = 1,680,062 (92.57%) number of supplementary alignments = 7,813 (0.43%) number of secondary alignments = 0 number of mapped bases = 98,723,508 bp number of sequenced bases = 98,694,104 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,592 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5079 >>>>>>> ACTG content number of A's = 24,547,494 bp (24.87%) number of C's = 18,070,142 bp (18.31%) number of T's = 31,965,333 bp (32.39%) number of G's = 24,098,673 bp (24.42%) number of N's = 12,462 bp (0.01%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 473,439 number of insertions = 5,754 mapped reads with insertion percentage = 0.34% number of deletions = 18,597 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.3091X There is a 2.88% of reference with a coverageData >= 1X There is a 0.21% 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 8148853 0.03269341102263493 0.6253938704843987 chr2 243199373 6545081 0.026912409021712404 0.30644826879443615 chr3 198022430 7162731 0.03617131150243939 0.203224275125413 chr4 191154276 5516531 0.02885905100025071 0.19370988841175288 chr5 180915260 6104961 0.03374486486104047 0.19795924585777624 chr6 171115067 6560283 0.038338429894078235 0.2338432163374855 chr7 159138663 4565255 0.028687277585083142 0.40660886417058434 chr8 146364022 10664965 0.07286602851074972 0.423181386346329 chr9 141213431 4038086 0.02859562274922702 0.25511140619343187 chr10 135534747 5046989 0.0372376022511777 0.28800904048426057 chr11 135006516 4807505 0.03560942939968912 0.273339209269264 chr12 133851895 3797355 0.028369826217253032 0.18729718992738115 chr13 115169878 2450019 0.021273088437238772 0.15686030747374205 chr14 107349540 1699034 0.01582711952002775 0.14734690879987256 chr15 102531392 2873353 0.02802412942955071 0.17992424687520855 chr16 90354753 2726188 0.03017204861375693 0.199604644394041 chr17 81195210 2714421 0.03343080213721967 0.22347821226695005 chr18 78077248 2356269 0.030178689187405787 0.4396118873087121 chr19 59128983 1427684 0.02414524870147014 0.42587927764063604 chr20 63025520 2109930 0.033477391380507454 0.19906749488703043 chr21 48129895 1443365 0.02998894969540241 0.19851101585072056 chr22 51304566 602909 0.01175156612766201 0.11514722677428407 chrMT 16571 14760 0.8907126908454529 0.9593091784421062 chrX 155270560 5107187 0.032892178658980815 0.22614031340952223 chrY 59373566 239794 0.0040387333312605815 0.10135356682760045