BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173861.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 = 2,553,744 number of mapped reads = 2,485,962 (97.35%) number of supplementary alignments = 269,374 (10.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,244,628 number of mapped paired reads (second in pair) = 1,241,334 number of mapped paired reads (both in pair) = 2,442,436 number of mapped paired reads (singletons) = 43,526 number of mapped bases = 292,614,850 bp number of sequenced bases = 292,447,034 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,897,049 duplication rate = 62.97% >>>>>>> Insert size mean insert size = 845,084.4987 std insert size = 8,550,010.9696 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.6277 >>>>>>> ACTG content number of A's = 88,421,231 bp (30.23%) number of C's = 56,941,242 bp (19.47%) number of T's = 88,158,173 bp (30.15%) number of G's = 58,922,988 bp (20.15%) number of N's = 3,400 bp (0%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,979,882 number of insertions = 31,330 mapped reads with insertion percentage = 1.22% number of deletions = 67,849 mapped reads with deletion percentage = 2.66% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.0945X std coverageData = 1.5277X There is a 2.13% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.97% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% 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 0.06% 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 0.02% 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% 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 26522274 0.10640805584993909 1.3125246509171882 chr2 243199373 25704209 0.1056919213356689 4.093846346170264 chr3 198022430 21189257 0.10700432774206436 0.9333659075592663 chr4 191154276 18160857 0.09500628173235319 0.9676602716889338 chr5 180915260 20517662 0.11341034471055675 0.9648388028143065 chr6 171115067 16686676 0.09751728057938931 0.9186677149742002 chr7 159138663 21270599 0.13366078738514978 1.5410706469439663 chr8 146364022 12754780 0.08714423002122748 0.9210661187674603 chr9 141213431 11410478 0.08080306468865557 0.9349425401580758 chr10 135534747 11667506 0.08608498011214792 1.5341078059475546 chr11 135006516 16413476 0.12157543566267572 0.988478827618406 chr12 133851895 10305866 0.0769945468459748 0.7853626718589884 chr13 115169878 9771596 0.08484506686722373 0.8309781822040759 chr14 107349540 7388907 0.06883035549104356 0.7383942771029828 chr15 102531392 6616376 0.06453024650245653 0.7076904817842327 chr16 90354753 11757341 0.13012421161729035 1.3419701431413738 chr17 81195210 6989714 0.08608529985943753 0.8945728519391449 chr18 78077248 4865102 0.06231139191791186 1.1888227331803252 chr19 59128983 5376125 0.0909219933649121 1.265061710752593 chr20 63025520 8710391 0.13820419093725844 1.0540351326744564 chr21 48129895 4567237 0.09489397390125202 0.8958346291303516 chr22 51304566 2663582 0.05191705549170809 0.610008445495834 chrMT 16571 746546 45.05135477641663 36.97000192239001 chrX 155270560 10116221 0.06515221559064384 0.7222174693934198 chrY 59373566 442072 0.007445602980962942 0.3583380424149351