BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173930.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 = 3,546,356 number of mapped reads = 3,472,213 (97.91%) number of supplementary alignments = 397,336 (11.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,737,190 number of mapped paired reads (second in pair) = 1,735,023 number of mapped paired reads (both in pair) = 3,430,022 number of mapped paired reads (singletons) = 42,191 number of mapped bases = 390,207,401 bp number of sequenced bases = 389,943,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,739,801 duplication rate = 63.65% >>>>>>> Insert size mean insert size = 815,579.8149 std insert size = 8,356,596.7002 median insert size = 145 >>>>>>> Mapping quality mean mapping quality = 52.7079 >>>>>>> ACTG content number of A's = 117,366,368 bp (30.1%) number of C's = 76,982,380 bp (19.74%) number of T's = 116,038,872 bp (29.76%) number of G's = 79,553,253 bp (20.4%) number of N's = 2,907 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 3,284,842 number of insertions = 43,492 mapped reads with insertion percentage = 1.21% number of deletions = 108,081 mapped reads with deletion percentage = 3.03% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.126X std coverageData = 2.3774X There is a 2.71% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 1.45% of reference with a coverageData >= 3X There is a 1.18% of reference with a coverageData >= 4X There is a 0.89% of reference with a coverageData >= 5X There is a 0.75% of reference with a coverageData >= 6X There is a 0.57% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 30973269 0.12426556401638815 1.3840187365368826 chr2 243199373 35106748 0.1443537767673439 7.296410014843333 chr3 198022430 26421424 0.13342642043126124 1.133874194519294 chr4 191154276 25330054 0.1325110509167998 1.2979110704072103 chr5 180915260 24534994 0.13561594527736356 1.1357774116239623 chr6 171115067 21432909 0.12525436465510076 1.1977562086938085 chr7 159138663 22549913 0.14169977662813468 1.4406240679994515 chr8 146364022 21398945 0.14620358683502152 1.7632255702815165 chr9 141213431 15691969 0.11112235492670665 1.308518018000313 chr10 135534747 20223197 0.14921042350859295 1.6733983214218764 chr11 135006516 17803705 0.1318729312294823 1.1428486457269416 chr12 133851895 17629180 0.1317066149866612 1.1684875172487323 chr13 115169878 13475972 0.11700951875628451 1.0768235677304485 chr14 107349540 11984976 0.11164440946835916 1.0278926314653796 chr15 102531392 10700282 0.10436103315558225 0.9974128221577985 chr16 90354753 11883505 0.13152052997145597 1.2357305794637614 chr17 81195210 11353694 0.13983206644825477 1.181089148374556 chr18 78077248 11243140 0.14400020861391016 1.5365440506431753 chr19 59128983 7466733 0.12627873203907464 1.2099919483355843 chr20 63025520 8296129 0.13163126619185372 1.1245250679775998 chr21 48129895 5753355 0.11953807503631579 1.2153222109701374 chr22 51304566 4923317 0.09596255038976453 1.0599903298727893 chrMT 16571 502231 30.307826926558445 31.13383499702646 chrX 155270560 10534068 0.06784330526018584 0.7886293135769339 chrY 59373566 2993692 0.05042129354332532 0.8448495711904674