BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240024.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,666,838 number of mapped reads = 1,346,266 (80.77%) number of supplementary alignments = 7,142 (0.43%) number of secondary alignments = 0 number of mapped bases = 84,314,300 bp number of sequenced bases = 84,274,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,701 duplication rate = 8.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8887 >>>>>>> ACTG content number of A's = 22,943,311 bp (27.22%) number of C's = 14,965,410 bp (17.76%) number of T's = 27,208,924 bp (32.29%) number of G's = 19,097,704 bp (22.66%) number of N's = 59,362 bp (0.07%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 783,472 number of insertions = 5,994 mapped reads with insertion percentage = 0.44% number of deletions = 23,092 mapped reads with deletion percentage = 1.7% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2728X There is a 1.93% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% 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 6461394 0.02592328145092164 0.37235823733702117 chr2 243199373 8191002 0.033680193739644225 0.3470696110951809 chr3 198022430 6277643 0.03170167642120138 0.23818626883187452 chr4 191154276 5414129 0.028323347577116194 0.22964236695302034 chr5 180915260 5081040 0.028085193034573203 0.2251316228649404 chr6 171115067 4444788 0.025975433244578048 0.23963767750126597 chr7 159138663 4779299 0.030032293283750913 0.3309631344966026 chr8 146364022 4370074 0.029857569778999376 0.36231778279156374 chr9 141213431 3354348 0.02375374619996309 0.26111551787248094 chr10 135534747 3751738 0.02768100493078723 0.253163687051775 chr11 135006516 3839111 0.02843648672483334 0.2574934279670538 chr12 133851895 3855614 0.028805075938596162 0.2267220177490444 chr13 115169878 2364506 0.020530593945753767 0.1927370664222492 chr14 107349540 2693403 0.025090028331746925 0.21556207777477038 chr15 102531392 2192317 0.021381910039805174 0.2001875862042599 chr16 90354753 2347225 0.025977880765165724 0.2206096029409468 chr17 81195210 2002298 0.024660297079101095 0.21568478155816323 chr18 78077248 1953336 0.02501799243743837 0.365497174004171 chr19 59128983 1376297 0.02327618251103693 0.2733569718533119 chr20 63025520 1678266 0.026628356259496153 0.21956655839632438 chr21 48129895 1150730 0.02390884085660274 0.21050063035911515 chr22 51304566 935205 0.01822849451645298 0.17600765396239798 chrMT 16571 28818 1.739062217126305 2.218979396590383 chrX 155270560 5575317 0.03590710949970168 0.27532355727209445 chrY 59373566 196402 0.0033079030489763742 0.0783764929335358