BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174021.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 = 1,983,720 number of mapped reads = 1,937,523 (97.67%) number of supplementary alignments = 179,810 (9.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 966,750 number of mapped paired reads (second in pair) = 970,773 number of mapped paired reads (both in pair) = 1,907,822 number of mapped paired reads (singletons) = 29,701 number of mapped bases = 230,396,283 bp number of sequenced bases = 230,287,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,495,160 duplication rate = 65.52% >>>>>>> Insert size mean insert size = 732,817.1476 std insert size = 8,010,926.7715 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.8656 >>>>>>> ACTG content number of A's = 69,408,525 bp (30.14%) number of C's = 45,306,812 bp (19.67%) number of T's = 69,101,953 bp (30.01%) number of G's = 46,467,071 bp (20.18%) number of N's = 2,986 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 2,285,786 number of insertions = 23,467 mapped reads with insertion percentage = 1.17% number of deletions = 40,441 mapped reads with deletion percentage = 2.03% homopolymer indels = 44.77% >>>>>>> Coverage mean coverageData = 0.0744X std coverageData = 1.2228X There is a 1.59% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.79% of reference with a coverageData >= 4X There is a 0.59% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% 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 0.04% 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 16748945 0.06719720469623224 0.849225966544982 chr2 243199373 19451873 0.07998323663441352 3.2514788719941268 chr3 198022430 20079443 0.10139984142200457 0.9205307952541808 chr4 191154276 11382441 0.059545835113832345 0.746167028999194 chr5 180915260 13509642 0.07467386664894934 0.7835497986445209 chr6 171115067 11922935 0.06967787938861048 0.8080993643203216 chr7 159138663 13129083 0.08250090048827417 0.9341093401802353 chr8 146364022 14080774 0.09620379248665359 1.020188721833009 chr9 141213431 10088446 0.07144112233913501 0.827965724147821 chr10 135534747 12051885 0.08892099824408865 1.159624869890917 chr11 135006516 8079916 0.05984834094970646 0.7005030735175866 chr12 133851895 11056517 0.08260261836412551 0.8286286396037778 chr13 115169878 5891275 0.05115291517457368 0.6583892170496412 chr14 107349540 7251776 0.06755293036188138 0.7450485217628662 chr15 102531392 7650620 0.07461734255982792 0.779379448145793 chr16 90354753 7750375 0.08577716990715474 0.9013919749631406 chr17 81195210 9210337 0.11343448708365925 0.985822025128618 chr18 78077248 4352084 0.05574074537053355 0.8810977715072978 chr19 59128983 3569703 0.060371459458384395 0.7653926409635552 chr20 63025520 9929829 0.1575525120617807 1.1697194320077209 chr21 48129895 3061391 0.0636068497552301 0.7363025584230002 chr22 51304566 1602332 0.031231762100862523 0.48275418144408966 chrMT 16571 579032 34.94248989197997 36.012430560145 chrX 155270560 7622933 0.04909451604991957 0.6274108258808695 chrY 59373566 342696 0.005771861504831965 0.2830034336653688