BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524932.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 = 1,521,288 number of mapped reads = 1,409,072 (92.62%) number of supplementary alignments = 5,372 (0.35%) number of secondary alignments = 0 number of mapped bases = 82,389,681 bp number of sequenced bases = 82,362,857 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,403 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9069 >>>>>>> ACTG content number of A's = 21,755,414 bp (26.41%) number of C's = 15,548,010 bp (18.88%) number of T's = 25,024,619 bp (30.38%) number of G's = 20,034,165 bp (24.32%) number of N's = 649 bp (0%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 413,573 number of insertions = 6,602 mapped reads with insertion percentage = 0.47% number of deletions = 15,931 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.14% >>>>>>> Coverage mean coverageData = 0.0266X std coverageData = 0.2524X There is a 2.34% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% 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 8455588 0.03392403985224173 0.4506633359714383 chr2 243199373 7791108 0.03203588851357771 0.3019267645711351 chr3 198022430 5298624 0.026757696085236406 0.1829860978791311 chr4 191154276 3724364 0.019483550553689943 0.18593376041889567 chr5 180915260 5065069 0.027996914135380288 0.18498058076451238 chr6 171115067 5274987 0.030827133416603227 0.2031548779594513 chr7 159138663 5021590 0.03155480827434123 0.31835331523111826 chr8 146364022 7278970 0.04973196213479293 0.3279863687325342 chr9 141213431 2910250 0.02060887536965234 0.19951368716145645 chr10 135534747 3569629 0.026337371626185276 0.2785075455480141 chr11 135006516 4141847 0.030678867381482535 0.22480872167351557 chr12 133851895 2518414 0.018814929740068306 0.15800810263451442 chr13 115169878 1938704 0.016833429310396594 0.14403481136697477 chr14 107349540 1515252 0.01411512336242894 0.14026420362323008 chr15 102531392 2355764 0.022976026698242818 0.16924477625119472 chr16 90354753 2443039 0.02703830090709229 0.19436915430076102 chr17 81195210 1844532 0.022717251424067997 0.1719565082260882 chr18 78077248 2145870 0.027483934884590194 0.3328104903645541 chr19 59128983 1779126 0.030088899042961723 0.3269124377604854 chr20 63025520 1251541 0.019857686219804296 0.16278906269753682 chr21 48129895 730064 0.015168618173798219 0.16320730185002386 chr22 51304566 1506441 0.02936270818468672 0.19251723601753287 chrMT 16571 6039 0.36443183875445057 0.7106267744136441 chrX 155270560 3586336 0.023097334098621143 0.1820532275476221 chrY 59373566 236533 0.003983809899509826 0.14634025325432282