BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926986.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 17,739,428 number of mapped reads = 17,407,500 (98.13%) number of supplementary alignments = 307,013 (1.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,751,613 number of mapped paired reads (second in pair) = 8,655,887 number of mapped paired reads (both in pair) = 17,210,056 number of mapped paired reads (singletons) = 197,444 number of mapped bases = 1,626,611,444 bp number of sequenced bases = 1,625,402,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,037,394 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 197,789.4403 std insert size = 4,417,942.173 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.9986 >>>>>>> ACTG content number of A's = 462,830,705 bp (28.47%) number of C's = 325,038,280 bp (20%) number of T's = 470,035,560 bp (28.92%) number of G's = 367,370,702 bp (22.6%) number of N's = 126,776 bp (0.01%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 15,050,916 number of insertions = 271,546 mapped reads with insertion percentage = 1.53% number of deletions = 833,841 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.16% >>>>>>> Coverage mean coverageData = 0.5254X std coverageData = 2.0513X There is a 26.38% of reference with a coverageData >= 1X There is a 12.46% of reference with a coverageData >= 2X There is a 5.9% of reference with a coverageData >= 3X There is a 3.07% of reference with a coverageData >= 4X There is a 1.65% of reference with a coverageData >= 5X There is a 0.92% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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% 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 134957534 0.5414531504818196 2.50050270909511 chr2 243199373 144115171 0.59258035587123 3.6754241870849023 chr3 198022430 110050285 0.5557465636594804 1.2065656736497394 chr4 191154276 98687049 0.5162691155284437 1.8163773441652753 chr5 180915260 99057514 0.5475354262542584 1.1835527690481897 chr6 171115067 92584525 0.5410658840463184 1.4109245647934545 chr7 159138663 84558349 0.5313501282840362 1.677837321380861 chr8 146364022 84278122 0.575811738761866 1.4252740232477412 chr9 141213431 67518393 0.4781301078932074 2.4093378814396536 chr10 135534747 78612586 0.5800179491979278 3.026177751466924 chr11 135006516 69823960 0.5171895555026396 2.517219213488782 chr12 133851895 74896238 0.5595455932842789 1.443613816034158 chr13 115169878 48197551 0.4184909443075037 1.1001556006648305 chr14 107349540 49742241 0.46336706240194414 1.1507913275980204 chr15 102531392 48796773 0.475920321066157 1.191808655963802 chr16 90354753 51858661 0.5739450253380693 2.7704442089567767 chr17 81195210 42903806 0.5284031656547228 1.5103077847327722 chr18 78077248 43261278 0.5540830281313194 2.3492946845063467 chr19 59128983 26327926 0.4452626218854466 1.6317819305486196 chr20 63025520 38392193 0.6091531335243248 1.3677435511385345 chr21 48129895 20969237 0.4356800903056198 1.7131628158396917 chr22 51304566 21073344 0.4107498736077409 1.1188769059940769 chrMT 16571 145125 8.75776959748959 7.823183713339485 chrX 155270560 92866201 0.5980927807563777 1.4893849226601656 chrY 59373566 2937382 0.04947289169055468 1.5550089653610792