BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174009.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 = 2,229,952 number of mapped reads = 2,181,943 (97.85%) number of supplementary alignments = 206,254 (9.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,089,663 number of mapped paired reads (second in pair) = 1,092,280 number of mapped paired reads (both in pair) = 2,151,478 number of mapped paired reads (singletons) = 30,465 number of mapped bases = 260,682,598 bp number of sequenced bases = 260,552,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,727,089 duplication rate = 65.62% >>>>>>> Insert size mean insert size = 729,978.2384 std insert size = 7,816,628.6635 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.8252 >>>>>>> ACTG content number of A's = 78,451,290 bp (30.11%) number of C's = 51,231,086 bp (19.66%) number of T's = 78,139,965 bp (29.99%) number of G's = 52,726,937 bp (20.24%) number of N's = 3,462 bp (0%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 2,588,474 number of insertions = 27,753 mapped reads with insertion percentage = 1.23% number of deletions = 50,470 mapped reads with deletion percentage = 2.26% homopolymer indels = 44.96% >>>>>>> Coverage mean coverageData = 0.0842X std coverageData = 1.3697X There is a 1.67% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.87% of reference with a coverageData >= 4X There is a 0.68% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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% 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 18534514 0.07436095414983941 1.006551566631976 chr2 243199373 20140321 0.08281403340624567 3.559770873254769 chr3 198022430 24110184 0.12175481333099487 1.056978801024358 chr4 191154276 11518838 0.06025937918333566 0.8136690198633558 chr5 180915260 15557537 0.08599350325671809 0.8715689725066422 chr6 171115067 15145634 0.08851139917445143 0.9601056094527102 chr7 159138663 15397657 0.09675622950282044 1.0977403651640822 chr8 146364022 14151591 0.09668763406897905 1.0860100515861353 chr9 141213431 11715525 0.08296324872950647 0.9727024215263513 chr10 135534747 10971692 0.0809511379395573 1.2508820113265187 chr11 135006516 9622057 0.07127105627997984 0.7943599838720242 chr12 133851895 12453398 0.09303863796623874 0.9101314046262788 chr13 115169878 6099072 0.052957180348840865 0.6934491995423321 chr14 107349540 8061428 0.07509513315101303 0.816854040635591 chr15 102531392 9913578 0.09668822208129194 0.920820488090543 chr16 90354753 8773091 0.09709606532818478 1.0417999874919153 chr17 81195210 11745971 0.1446633489832713 1.1766481168978555 chr18 78077248 4460336 0.05712721841835409 1.071769989489016 chr19 59128983 4807824 0.08131078459441793 0.9451714678053709 chr20 63025520 11793647 0.18712494557760095 1.3339187912132975 chr21 48129895 3240623 0.06733077227781195 0.7802138661689916 chr22 51304566 2225331 0.0433749113090636 0.5925478782261406 chrMT 16571 956250 57.70623378190815 57.49945339866893 chrX 155270560 8829186 0.056863232798284494 0.7113797945108151 chrY 59373566 457313 0.007702299706909974 0.3515748873794077