BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124972.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,299,298 number of mapped reads = 2,258,264 (98.22%) number of supplementary alignments = 44,758 (1.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,136,128 number of mapped paired reads (second in pair) = 1,122,136 number of mapped paired reads (both in pair) = 2,242,274 number of mapped paired reads (singletons) = 15,990 number of mapped bases = 289,565,423 bp number of sequenced bases = 289,312,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 321,157 duplication rate = 12.82% >>>>>>> Insert size mean insert size = 89,642.7326 std insert size = 2,850,733.966 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 53.4979 >>>>>>> ACTG content number of A's = 83,891,932 bp (29%) number of C's = 56,485,608 bp (19.52%) number of T's = 85,752,864 bp (29.64%) number of G's = 63,180,060 bp (21.84%) number of N's = 2,123 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 2,839,266 number of insertions = 60,096 mapped reads with insertion percentage = 2.49% number of deletions = 122,679 mapped reads with deletion percentage = 5.2% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.0935X std coverageData = 1.0232X There is a 5.82% of reference with a coverageData >= 1X There is a 2.4% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 26109427 0.10475170290548644 0.7547128815896215 chr2 243199373 23850308 0.09806895349191545 1.1225589531699915 chr3 198022430 19814450 0.1000616445318846 0.4363006923250157 chr4 191154276 14277423 0.07469057610827393 1.34947930118614 chr5 180915260 15852247 0.08762249795843645 0.40347885354262086 chr6 171115067 16933449 0.09895942710877705 0.5454258857399532 chr7 159138663 20768653 0.1305066450130978 0.9072274106883351 chr8 146364022 19597454 0.13389529566220856 0.578352300836224 chr9 141213431 10943516 0.07749628291376902 1.1000244196365208 chr10 135534747 14034970 0.1035525598465167 2.864999328505792 chr11 135006516 9949432 0.07369593923896237 0.4633340265402794 chr12 133851895 13989234 0.10451278257958171 0.43898807678760876 chr13 115169878 6285947 0.05457978343955526 0.30876397260154975 chr14 107349540 12027987 0.11204507257320338 0.47045362481643616 chr15 102531392 7898167 0.07703169581468279 0.38071823017389345 chr16 90354753 10451730 0.11567437963114126 1.564776422653931 chr17 81195210 6374214 0.07850480342374877 0.8329452449984299 chr18 78077248 4120364 0.05277291535685274 1.0036549299119282 chr19 59128983 5127931 0.08672449177757717 0.5067109447402321 chr20 63025520 6860223 0.10884833635644736 0.6403484386496551 chr21 48129895 2842904 0.059067321879675824 0.7357133638641794 chr22 51304566 2520922 0.049136406299587446 0.31015622584535346 chrMT 16571 18956 1.143926136020759 1.496270981293261 chrX 155270560 13861563 0.08927360730842988 0.4452806872415447 chrY 59373566 5053952 0.08512124739147384 2.2423614245612455