BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716543.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,545,157 number of mapped reads = 1,274,153 (82.46%) number of supplementary alignments = 6,325 (0.41%) number of secondary alignments = 0 number of mapped bases = 73,325,111 bp number of sequenced bases = 73,304,170 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,633 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0919 >>>>>>> ACTG content number of A's = 18,667,772 bp (25.47%) number of C's = 13,587,553 bp (18.54%) number of T's = 23,713,157 bp (32.35%) number of G's = 17,333,652 bp (23.65%) number of N's = 2,036 bp (0%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 365,805 number of insertions = 5,584 mapped reads with insertion percentage = 0.44% number of deletions = 13,192 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.226X There is a 2.14% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5923553 0.023765449314567606 0.37741921510312104 chr2 243199373 6164719 0.025348416502702087 0.3160812257112162 chr3 198022430 4944594 0.02496986831239269 0.17196488606593022 chr4 191154276 4731881 0.024754251377562698 0.18330240771291997 chr5 180915260 4415964 0.0244090188964712 0.17029342912810508 chr6 171115067 4225956 0.024696574498609174 0.1932360181088697 chr7 159138663 4058212 0.025501106541280922 0.2590061988525754 chr8 146364022 3702802 0.02529858054870889 0.21355422095685558 chr9 141213431 3067198 0.021720299395600693 0.1896961502472084 chr10 135534747 3510559 0.025901542428820853 0.22454158102417396 chr11 135006516 3324097 0.02462175233082824 0.19929415432757433 chr12 133851895 3340510 0.02495676284597988 0.17494489874521843 chr13 115169878 2282558 0.0198190537286147 0.15485022526849837 chr14 107349540 2205274 0.020542929201187075 0.15913050295312586 chr15 102531392 2070109 0.020190001906928174 0.15722166006090738 chr16 90354753 2136575 0.02364651475501239 0.17798387879891236 chr17 81195210 1994306 0.024561867627412998 0.17607389008237948 chr18 78077248 1933933 0.024769482141583678 0.2974868090668153 chr19 59128983 1531312 0.025897824084002933 0.28490229165971537 chr20 63025520 1565705 0.024842397174985625 0.17420345688341277 chr21 48129895 972789 0.020211741579739578 0.16626356932226113 chr22 51304566 864343 0.016847291915499295 0.14037148089120555 chrMT 16571 4304 0.2597308551083218 0.5798769010937146 chrX 155270560 4137563 0.02664744044202584 0.1918609274809396 chrY 59373566 216295 0.003642951140916818 0.10029231891437973