BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173845.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 = 3,587,812 number of mapped reads = 3,488,248 (97.22%) number of supplementary alignments = 359,279 (10.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,750,037 number of mapped paired reads (second in pair) = 1,738,211 number of mapped paired reads (both in pair) = 3,419,852 number of mapped paired reads (singletons) = 68,396 number of mapped bases = 409,691,967 bp number of sequenced bases = 409,423,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,667,086 duplication rate = 63.9% >>>>>>> Insert size mean insert size = 1,063,072.7828 std insert size = 9,789,703.6625 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.6894 >>>>>>> ACTG content number of A's = 122,572,146 bp (29.94%) number of C's = 80,446,744 bp (19.65%) number of T's = 122,586,976 bp (29.94%) number of G's = 83,812,763 bp (20.47%) number of N's = 4,946 bp (0%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 4,377,034 number of insertions = 43,341 mapped reads with insertion percentage = 1.2% number of deletions = 116,016 mapped reads with deletion percentage = 3.25% homopolymer indels = 41.6% >>>>>>> Coverage mean coverageData = 0.1323X std coverageData = 2.0541X There is a 2.95% of reference with a coverageData >= 1X There is a 2.28% of reference with a coverageData >= 2X There is a 1.73% of reference with a coverageData >= 3X There is a 1.4% of reference with a coverageData >= 4X There is a 1.04% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.6% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% 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 0.02% 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 36316612 0.1457031956602427 1.7044563959075008 chr2 243199373 43555780 0.17909495186075172 5.873455069444373 chr3 198022430 31767823 0.1604253770646083 1.1272621783177015 chr4 191154276 25125550 0.13144121348350063 1.2093805267129847 chr5 180915260 25175313 0.1391552763431896 1.0416425418525472 chr6 171115067 23706569 0.13854168084450447 1.0955454488530554 chr7 159138663 25150145 0.158039187497761 1.628121195667808 chr8 146364022 17505790 0.11960446126576106 1.1071821230962924 chr9 141213431 14610843 0.1034663834490361 1.0735747863155303 chr10 135534747 16778465 0.1237945646513805 2.13963564839969 chr11 135006516 20418363 0.15123983349070352 1.1204910998707684 chr12 133851895 16057966 0.11996816331961531 0.9630538130531487 chr13 115169878 13342628 0.11585171601900976 0.9537829137707493 chr14 107349540 10033297 0.09346380990547327 0.860656696429542 chr15 102531392 13759971 0.13420251819072154 1.0046706162192827 chr16 90354753 16442196 0.1819737806156141 1.5075643004918868 chr17 81195210 9978358 0.12289343176771142 1.0358041044904462 chr18 78077248 6544245 0.08381756744295085 1.450365887055041 chr19 59128983 7865432 0.13302160126785878 1.6296260213517104 chr20 63025520 12626794 0.20034414630771788 1.2713882538901138 chr21 48129895 4490968 0.09330932469310395 0.8958583521645226 chr22 51304566 3571414 0.06961201075163563 0.6922108446128908 chrMT 16571 1288841 77.77689940257076 55.29900883865911 chrX 155270560 12922589 0.08322626646030001 0.8074792007852203 chrY 59373566 656015 0.011048940533570108 0.49499050224221686