BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354872.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 25,710,216 number of mapped reads = 25,472,926 (99.08%) number of supplementary alignments = 1,151,565 (4.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,746,788 number of mapped paired reads (second in pair) = 12,726,138 number of mapped paired reads (both in pair) = 25,430,592 number of mapped paired reads (singletons) = 42,334 number of mapped bases = 3,134,104,285 bp number of sequenced bases = 3,132,533,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,293,231 duplication rate = 63.49% >>>>>>> Insert size mean insert size = 435,734.314 std insert size = 7,602,506.9712 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.5463 >>>>>>> ACTG content number of A's = 854,324,379 bp (27.27%) number of C's = 681,439,391 bp (21.75%) number of T's = 872,940,071 bp (27.87%) number of G's = 723,738,140 bp (23.1%) number of N's = 91,902 bp (0%) GC percentage = 44.86% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 18,258,642 number of insertions = 529,975 mapped reads with insertion percentage = 1.93% number of deletions = 532,060 mapped reads with deletion percentage = 1.98% homopolymer indels = 42.4% >>>>>>> Coverage mean coverageData = 1.0124X std coverageData = 56.9371X There is a 25.74% of reference with a coverageData >= 1X There is a 21.19% of reference with a coverageData >= 2X There is a 12.79% of reference with a coverageData >= 3X There is a 10.74% of reference with a coverageData >= 4X There is a 6.36% of reference with a coverageData >= 5X There is a 5.43% of reference with a coverageData >= 6X There is a 3.2% of reference with a coverageData >= 7X There is a 2.73% of reference with a coverageData >= 8X There is a 1.62% of reference with a coverageData >= 9X There is a 1.38% of reference with a coverageData >= 10X There is a 0.82% of reference with a coverageData >= 11X There is a 0.7% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% 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 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 257677306 1.0338080802615133 29.759163188103187 chr2 243199373 303878217 1.2495024689064473 196.24663442519577 chr3 198022430 199781542 1.0088833977039873 3.106249744540252 chr4 191154276 206641310 1.0810185067479212 16.432942339627612 chr5 180915260 182634177 1.0095012272596573 2.342511552632207 chr6 171115067 170275426 0.9950931205841739 4.278388159715701 chr7 159138663 166581501 1.0467695144579667 18.940404317772476 chr8 146364022 151833769 1.0373708437719755 4.532818817893419 chr9 141213431 133050623 0.942195243453861 13.921131998582466 chr10 135534747 175957314 1.2982450470800673 40.14445028946056 chr11 135006516 141932219 1.0512990276706349 5.605371467298968 chr12 133851895 133195110 0.995093196103051 2.3225100848714497 chr13 115169878 94827802 0.8233732955764701 2.037493427423168 chr14 107349540 94556020 0.8808237091654049 7.486019349310677 chr15 102531392 92178162 0.8990238033635591 2.1558819989308233 chr16 90354753 103350301 1.143828050750136 7.686717302005755 chr17 81195210 90848357 1.1188881339182446 6.9525293404738875 chr18 78077248 85603011 1.0963886816297623 13.326588230761304 chr19 59128983 69369711 1.1731930346239847 16.141699942820043 chr20 63025520 67064941 1.0640918313724346 5.945461953916914 chr21 48129895 44347462 0.9214119831343908 8.897627552812478 chr22 51304566 42233274 0.8231874332588643 3.1654812553923453 chrMT 16571 3942563 237.91943757166135 64.09795738081358 chrX 155270560 82906284 0.5339472209026618 2.640662677823678 chrY 59373566 39437883 0.6642330191183059 20.917054862744862