BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174003.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 = 4,577,328 number of mapped reads = 4,457,508 (97.38%) number of supplementary alignments = 447,298 (9.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,231,278 number of mapped paired reads (second in pair) = 2,226,230 number of mapped paired reads (both in pair) = 4,380,228 number of mapped paired reads (singletons) = 77,280 number of mapped bases = 525,974,825 bp number of sequenced bases = 525,669,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,405,144 duplication rate = 63.78% >>>>>>> Insert size mean insert size = 1,063,770.2368 std insert size = 9,682,241.1931 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.9483 >>>>>>> ACTG content number of A's = 158,874,913 bp (30.22%) number of C's = 102,205,691 bp (19.44%) number of T's = 158,507,603 bp (30.15%) number of G's = 106,075,204 bp (20.18%) number of N's = 5,737 bp (0%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 5,517,940 number of insertions = 61,989 mapped reads with insertion percentage = 1.34% number of deletions = 121,881 mapped reads with deletion percentage = 2.66% homopolymer indels = 42.77% >>>>>>> Coverage mean coverageData = 0.1699X std coverageData = 2.5648X There is a 3.77% of reference with a coverageData >= 1X There is a 2.9% of reference with a coverageData >= 2X There is a 2.19% of reference with a coverageData >= 3X There is a 1.76% of reference with a coverageData >= 4X There is a 1.32% of reference with a coverageData >= 5X There is a 1.05% of reference with a coverageData >= 6X There is a 0.77% of reference with a coverageData >= 7X There is a 0.62% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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% 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 41555922 0.16672344419153926 1.8177543485716614 chr2 243199373 46334705 0.1905214821421435 7.42662373147871 chr3 198022430 36400314 0.18381914614420194 1.2157655378497267 chr4 191154276 36841104 0.1927296881394377 1.883745759869557 chr5 180915260 32881256 0.1817494886832653 1.2103812480604559 chr6 171115067 32111353 0.18765941283241877 1.4009782391418224 chr7 159138663 29025007 0.18238815415962115 1.6384281241842922 chr8 146364022 27043764 0.18477057155480464 2.255476328937113 chr9 141213431 22649115 0.16038924087893594 1.6734366863838022 chr10 135534747 25327811 0.1868731934844723 2.123877721113269 chr11 135006516 23713277 0.175645425884481 1.2188533137149835 chr12 133851895 24236089 0.18106646155439188 1.2114916488049794 chr13 115169878 18750046 0.16280338510039927 1.1568077280908895 chr14 107349540 16008982 0.14912948858467395 1.1030740268251604 chr15 102531392 14992106 0.14621966704597164 1.0644457200019253 chr16 90354753 15670935 0.1734378599872881 1.4599639327741833 chr17 81195210 14197088 0.17485129972568578 1.3279270302179103 chr18 78077248 14926769 0.1911794970027632 2.5122412673891006 chr19 59128983 9108292 0.15404107322461474 1.4225838248716736 chr20 63025520 11156735 0.1770193248703065 1.2689732990400924 chr21 48129895 7461993 0.15503863035645518 1.5604862936099755 chr22 51304566 5940383 0.11578663388361964 1.0484620149365573 chrMT 16571 1073739 64.796270593205 49.38561415364193 chrX 155270560 14094504 0.09077383375187158 0.8468679895162826 chrY 59373566 4473536 0.07534558392534482 1.4912645011424372