BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173893.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 = 2,875,858 number of mapped reads = 2,795,867 (97.22%) number of supplementary alignments = 273,896 (9.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,401,459 number of mapped paired reads (second in pair) = 1,394,408 number of mapped paired reads (both in pair) = 2,742,374 number of mapped paired reads (singletons) = 53,493 number of mapped bases = 329,056,473 bp number of sequenced bases = 328,869,453 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,059,128 duplication rate = 62.73% >>>>>>> Insert size mean insert size = 941,482.178 std insert size = 8,996,458.5653 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.6522 >>>>>>> ACTG content number of A's = 98,503,786 bp (29.95%) number of C's = 65,000,574 bp (19.76%) number of T's = 98,233,733 bp (29.87%) number of G's = 67,127,135 bp (20.41%) number of N's = 4,225 bp (0%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 3,464,728 number of insertions = 35,867 mapped reads with insertion percentage = 1.24% number of deletions = 73,926 mapped reads with deletion percentage = 2.58% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.1063X std coverageData = 1.6555X There is a 2.54% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 1.43% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.64% of reference with a coverageData >= 6X There is a 0.44% 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 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 26015281 0.10437398669510235 1.23749979928856 chr2 243199373 30934633 0.12719865441429407 4.591692456558205 chr3 198022430 26705403 0.134860495348936 0.9919863000038578 chr4 191154276 19175334 0.10031339293712686 1.0956419196819716 chr5 180915260 20610922 0.11392583466977854 0.9041818685087116 chr6 171115067 19662397 0.11490745581159138 0.9279703348701773 chr7 159138663 21982456 0.1381339743943934 1.5475714518386152 chr8 146364022 14636306 0.09999934273465101 0.996683673042544 chr9 141213431 14249085 0.10090460163098793 0.9556921836093956 chr10 135534747 12994881 0.09587859414383236 1.6077693153019583 chr11 135006516 16105192 0.11929196069321572 0.9416442701177228 chr12 133851895 12885859 0.09626952984117258 0.8288812388010338 chr13 115169878 7134064 0.061943835696344145 0.6663408544041376 chr14 107349540 8695933 0.0810057779474416 0.7663905891029754 chr15 102531392 11401453 0.11119963142605145 0.8856021056222589 chr16 90354753 13310561 0.1473144528434492 1.289700269610992 chr17 81195210 8582416 0.10570101364353883 0.9486294452164442 chr18 78077248 5771217 0.07391675741440067 1.1837617904285767 chr19 59128983 6263541 0.10593013243606778 1.3368608374085327 chr20 63025520 10709441 0.1699222949687682 1.1368056481312603 chr21 48129895 5537762 0.11505867610972349 0.9807399370872316 chr22 51304566 3010994 0.058688616525866336 0.6152380156155003 chrMT 16571 1284285 77.50196125761873 59.54379529013247 chrX 155270560 10844238 0.06984091510972847 0.7035636339067276 chrY 59373566 552819 0.009310860661460018 0.5959063670764037