BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695940.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 20,319,318 number of mapped reads = 20,161,142 (99.22%) number of supplementary alignments = 52,717 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,128,022 number of mapped paired reads (second in pair) = 10,033,120 number of mapped paired reads (both in pair) = 20,048,872 number of mapped paired reads (singletons) = 112,270 number of mapped bases = 2,000,350,119 bp number of sequenced bases = 1,999,977,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,866,643 duplication rate = 8.67% >>>>>>> Insert size mean insert size = 37,345.2407 std insert size = 1,893,924.4028 median insert size = 326 >>>>>>> Mapping quality mean mapping quality = 49.9757 >>>>>>> ACTG content number of A's = 593,928,540 bp (29.7%) number of C's = 404,316,421 bp (20.22%) number of T's = 594,131,034 bp (29.71%) number of G's = 406,719,405 bp (20.34%) number of N's = 882,384 bp (0.04%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 12,932,452 number of insertions = 127,470 mapped reads with insertion percentage = 0.62% number of deletions = 163,013 mapped reads with deletion percentage = 0.79% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.6462X std coverageData = 3.5438X There is a 11.65% of reference with a coverageData >= 1X There is a 7.49% of reference with a coverageData >= 2X There is a 5.69% of reference with a coverageData >= 3X There is a 4.57% of reference with a coverageData >= 4X There is a 3.79% of reference with a coverageData >= 5X There is a 3.2% of reference with a coverageData >= 6X There is a 2.74% of reference with a coverageData >= 7X There is a 2.37% of reference with a coverageData >= 8X There is a 2.07% of reference with a coverageData >= 9X There is a 1.81% of reference with a coverageData >= 10X There is a 1.6% of reference with a coverageData >= 11X There is a 1.42% of reference with a coverageData >= 12X There is a 1.27% of reference with a coverageData >= 13X There is a 1.13% of reference with a coverageData >= 14X There is a 1.02% of reference with a coverageData >= 15X There is a 0.92% of reference with a coverageData >= 16X There is a 0.83% of reference with a coverageData >= 17X There is a 0.76% of reference with a coverageData >= 18X There is a 0.69% of reference with a coverageData >= 19X There is a 0.63% of reference with a coverageData >= 20X There is a 0.58% of reference with a coverageData >= 21X There is a 0.53% of reference with a coverageData >= 22X There is a 0.49% of reference with a coverageData >= 23X There is a 0.45% of reference with a coverageData >= 24X There is a 0.42% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.36% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177814568 0.7133966899925999 3.5299256373309307 chr2 243199373 100647707 0.41384854639407315 3.1836493023338384 chr3 198022430 241477510 1.2194452416324757 4.540661926067792 chr4 191154276 103554908 0.5417347190287284 3.125353069783304 chr5 180915260 253986942 1.4039000469059382 6.229357932124999 chr6 171115067 82863888 0.4842582798392616 2.1436458564516823 chr7 159138663 111421715 0.7001549020177453 2.960862322821313 chr8 146364022 156392501 1.0685173778566976 4.427812738572589 chr9 141213431 29297777 0.20747160374568055 1.8759394478602314 chr10 135534747 132520036 0.9777569142472373 4.270779620278564 chr11 135006516 97168546 0.7197322683299227 3.7099777436516823 chr12 133851895 115994710 0.8665899724467853 4.002883619037778 chr13 115169878 70905398 0.6156592264515554 2.9727289148823917 chr14 107349540 51094632 0.475965076329158 2.498437706997564 chr15 102531392 29469026 0.2874146680852631 2.2986765894105905 chr16 90354753 51697216 0.5721582349962265 3.0007701236088993 chr17 81195210 14746587 0.18161892801311802 1.8882461740380754 chr18 78077248 34733643 0.44486254177401335 2.470339950412565 chr19 59128983 4112599 0.06955301429757384 0.9357940527518026 chr20 63025520 8534651 0.1354157966487226 0.9504508698853351 chr21 48129895 32449942 0.6742159316989992 2.8976404954035813 chr22 51304566 6930671 0.13508877552925797 2.256908638147875 chrMT 16571 4187 0.2526703276808883 0.5862395973387569 chrX 155270560 90660686 0.583888446077608 4.642591918773385 chrY 59373566 1870073 0.03149672701147847 0.3607111076579911