BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156420.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 = 10,014,390 number of mapped reads = 9,807,044 (97.93%) number of supplementary alignments = 1,389,112 (13.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,899,967 number of mapped paired reads (second in pair) = 4,907,077 number of mapped paired reads (both in pair) = 9,671,492 number of mapped paired reads (singletons) = 135,552 number of mapped bases = 1,114,017,936 bp number of sequenced bases = 1,113,215,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,050,885 duplication rate = 65.82% >>>>>>> Insert size mean insert size = 1,131,097.968 std insert size = 9,752,546.054 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.4603 >>>>>>> ACTG content number of A's = 331,593,101 bp (29.79%) number of C's = 221,551,592 bp (19.9%) number of T's = 329,271,314 bp (29.58%) number of G's = 230,791,437 bp (20.73%) number of N's = 8,258 bp (0%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 9,438,535 number of insertions = 124,177 mapped reads with insertion percentage = 1.22% number of deletions = 339,021 mapped reads with deletion percentage = 3.37% homopolymer indels = 40.93% >>>>>>> Coverage mean coverageData = 0.3599X std coverageData = 6.5527X There is a 7.31% of reference with a coverageData >= 1X There is a 5.58% of reference with a coverageData >= 2X There is a 4.25% of reference with a coverageData >= 3X There is a 3.45% of reference with a coverageData >= 4X There is a 2.63% of reference with a coverageData >= 5X There is a 2.18% of reference with a coverageData >= 6X There is a 1.66% of reference with a coverageData >= 7X There is a 1.43% of reference with a coverageData >= 8X There is a 1.09% of reference with a coverageData >= 9X There is a 0.98% of reference with a coverageData >= 10X There is a 0.74% of reference with a coverageData >= 11X There is a 0.68% of reference with a coverageData >= 12X There is a 0.51% of reference with a coverageData >= 13X There is a 0.47% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 91215605 0.3659593891242502 2.917926396588923 chr2 243199373 102612838 0.4219288756143298 21.763357357301352 chr3 198022430 77685634 0.3923072451943954 1.9328986367047316 chr4 191154276 73664963 0.38536916118999087 2.865046753307961 chr5 180915260 67917676 0.3754115379763985 1.8858418428737875 chr6 171115067 64738928 0.3783356377378504 2.295473637227677 chr7 159138663 63620126 0.39977793454253163 2.8135731571164158 chr8 146364022 54933155 0.3753187036633907 3.1912878071417756 chr9 141213431 46635837 0.3302507181487574 2.6177142548933756 chr10 135534747 53108854 0.39184677859766837 3.812064207606432 chr11 135006516 51544232 0.3817906981615613 1.9848933353929124 chr12 133851895 52441294 0.39178596612322897 2.0021969547988214 chr13 115169878 35987226 0.3124708181074916 1.7230322246863878 chr14 107349540 34307636 0.3195881044296976 1.7753456927844298 chr15 102531392 31568207 0.30788821242181125 1.7413099116208322 chr16 90354753 34451429 0.38129072191697544 2.6372029581364473 chr17 81195210 32350388 0.39842729638854313 2.3514723873985797 chr18 78077248 32011535 0.4099982494260044 3.644583745943116 chr19 59128983 21376562 0.3615242629828421 2.3573185908170484 chr20 63025520 25082817 0.39797873940587875 2.0907275019558456 chr21 48129895 16077212 0.33403796122970975 2.5785511735411633 chr22 51304566 13826459 0.26949763106854857 2.2818288422018127 chrMT 16571 1203267 72.61281757286827 60.594248669099116 chrX 155270560 27204587 0.17520763111822357 1.2995531018433293 chrY 59373566 8451469 0.14234396835790528 2.1805380140609794