BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004071.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 = 2,102,706 number of mapped reads = 1,914,923 (91.07%) number of supplementary alignments = 11,373 (0.54%) number of secondary alignments = 0 number of mapped bases = 130,476,294 bp number of sequenced bases = 130,420,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,305 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3951 >>>>>>> ACTG content number of A's = 37,074,078 bp (28.43%) number of C's = 24,355,068 bp (18.67%) number of T's = 40,892,876 bp (31.35%) number of G's = 28,073,958 bp (21.53%) number of N's = 24,037 bp (0.02%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,089,090 number of insertions = 9,116 mapped reads with insertion percentage = 0.47% number of deletions = 32,291 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.0421X std coverageData = 0.3346X There is a 3.65% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10323033 0.04141627795583306 0.6041788258749421 chr2 243199373 10462311 0.043019481797759405 0.3545540135710168 chr3 198022430 9067289 0.04578920175860886 0.2387690826790306 chr4 191154276 9461855 0.0494985265200136 0.2576314011120251 chr5 180915260 8605575 0.047566882970513376 0.24398183618700806 chr6 171115067 8019790 0.04686781906820631 0.26079057976274694 chr7 159138663 7533269 0.04733776731553915 0.4261495513430039 chr8 146364022 8249959 0.05636603099086741 0.4739936398100018 chr9 141213431 4923741 0.03486737037074044 0.29612935050606853 chr10 135534747 6286486 0.046382836424964886 0.32077849560108773 chr11 135006516 4732320 0.03505253035342383 0.2509166126171324 chr12 133851895 6003085 0.04484871133128149 0.24074972117130417 chr13 115169878 4287147 0.03722455102366263 0.22032284262540527 chr14 107349540 3081199 0.02870248908379114 0.20280520503297958 chr15 102531392 4467802 0.04357496677700426 0.23679115948804197 chr16 90354753 3487293 0.03859556785020485 0.23664839406753246 chr17 81195210 2690732 0.033139048473425955 0.21088742265715352 chr18 78077248 3626281 0.046444785041603924 0.5106298435742794 chr19 59128983 1830707 0.03096124619630275 0.4243668134886233 chr20 63025520 2771469 0.04397375856637121 0.23929267134806673 chr21 48129895 1717168 0.035677784046692806 0.22164686664366856 chr22 51304566 1071225 0.02087972053013761 0.15924061948234186 chrMT 16571 30148 1.8193229135236255 1.7241085014111965 chrX 155270560 7477445 0.048157519364907295 0.2633057707615197 chrY 59373566 268965 0.004530046249874902 0.09129664526943226