BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819091.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,361,107 number of mapped reads = 3,087,492 (91.86%) number of supplementary alignments = 14,538 (0.43%) number of secondary alignments = 0 number of mapped bases = 180,101,299 bp number of sequenced bases = 180,045,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,830 duplication rate = 4.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8623 >>>>>>> ACTG content number of A's = 45,885,764 bp (25.49%) number of C's = 33,965,932 bp (18.87%) number of T's = 57,595,874 bp (31.99%) number of G's = 42,595,396 bp (23.66%) number of N's = 2,627 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 909,950 number of insertions = 12,777 mapped reads with insertion percentage = 0.41% number of deletions = 33,456 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.4% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.4918X There is a 4.81% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17734454 0.07115109253830104 0.9900418763383892 chr2 243199373 14159957 0.058223657509182805 0.5692177652083197 chr3 198022430 10082901 0.05091797429210418 0.2702200370479537 chr4 191154276 10083227 0.05274915743972162 0.32637961396531795 chr5 180915260 9758363 0.05393886065774661 0.2755493039709099 chr6 171115067 7619329 0.044527516679755616 0.3567322559873017 chr7 159138663 9033741 0.05676647541018992 0.6566968929875749 chr8 146364022 16491973 0.11267777951606167 0.5087185705480388 chr9 141213431 7676010 0.05435750654624347 0.40694240565256057 chr10 135534747 9429755 0.06957444647017344 0.472047974007335 chr11 135006516 6106657 0.04523231308331814 0.4526841197253676 chr12 133851895 8358994 0.06244957533100297 0.2967694866124347 chr13 115169878 3940021 0.03421051639908831 0.21704277062664415 chr14 107349540 4282865 0.039896444828734244 0.24531776534875716 chr15 102531392 4854128 0.047342846959495095 0.27228348968999405 chr16 90354753 5601758 0.06199738048091394 0.32447912942079093 chr17 81195210 6361749 0.07835128451542893 0.3668535713429043 chr18 78077248 4157162 0.053244217828989054 0.7951400286673491 chr19 59128983 3721146 0.0629326907246147 0.6587754776232077 chr20 63025520 5065335 0.08036958679595187 0.3409131620180392 chr21 48129895 2498687 0.05191548828436048 0.3078590898256114 chr22 51304566 1487595 0.028995372458661867 0.19742345613393553 chrMT 16571 14852 0.8962645585661698 1.241776799802397 chrX 155270560 10986551 0.07075746361705658 0.37441908059102696 chrY 59373566 594089 0.010005951133202948 0.26578840879867593