BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238615.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,407,718 number of mapped reads = 2,785,494 (81.74%) number of supplementary alignments = 22,467 (0.66%) number of secondary alignments = 0 number of mapped bases = 175,165,165 bp number of sequenced bases = 175,086,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 637,395 duplication rate = 17.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2919 >>>>>>> ACTG content number of A's = 43,074,908 bp (24.6%) number of C's = 32,193,925 bp (18.39%) number of T's = 57,088,739 bp (32.61%) number of G's = 42,719,596 bp (24.4%) number of N's = 9,082 bp (0.01%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 937,678 number of insertions = 11,792 mapped reads with insertion percentage = 0.42% number of deletions = 45,305 mapped reads with deletion percentage = 1.61% homopolymer indels = 43.52% >>>>>>> Coverage mean coverageData = 0.0566X std coverageData = 0.7363X There is a 3.08% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 17279493 0.06932577712614807 1.127349142159663 chr2 243199373 14260820 0.05863839130868154 1.689841365917939 chr3 198022430 8876695 0.0448267148322541 0.36184303221591907 chr4 191154276 8153932 0.04265628878738763 0.34870263604481255 chr5 180915260 15317984 0.08466938609822079 0.4969163066119314 chr6 171115067 6271871 0.0366529441852131 0.6174493459033157 chr7 159138663 5910812 0.03714252645191571 0.43788384020657944 chr8 146364022 6957248 0.047533867305176954 0.6098590709574208 chr9 141213431 6715491 0.04755561105232264 0.4143283114151124 chr10 135534747 9626095 0.07102307867959498 0.5440129397661839 chr11 135006516 12270808 0.09089048709323037 0.5353835191901533 chr12 133851895 9304307 0.0695119557328643 0.44875727011599487 chr13 115169878 5493685 0.04770071042360573 0.47808123271010566 chr14 107349540 4692633 0.0437135827503313 0.35781872030161666 chr15 102531392 7700189 0.07510079449618708 0.5509778310953422 chr16 90354753 3871657 0.042849511192842284 0.3828513703819618 chr17 81195210 7923078 0.09758060851126563 0.5380347493061058 chr18 78077248 3867088 0.049528999792615644 1.138642110819905 chr19 59128983 6771896 0.11452752366804618 0.7794318143025578 chr20 63025520 3677375 0.058347396419736006 0.4245500143840988 chr21 48129895 1878051 0.03902046742466403 0.3543224638562039 chr22 51304566 3508782 0.06839122272274947 0.4486817570372007 chrMT 16571 140562 8.482409027819685 5.982219832833257 chrX 155270560 4331761 0.027898147594753314 0.2912383424396649 chrY 59373566 362852 0.0061113391774379865 0.25183677103831537