BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5038420.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 74,793,292
number of mapped reads = 74,310,262 (99.35%)
number of supplementary alignments = 109,908 (0.15%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 37,319,936
number of mapped paired reads (second in pair) = 36,990,326
number of mapped paired reads (both in pair) = 73,938,498
number of mapped paired reads (singletons) = 371,764
number of mapped bases = 11,040,816,503 bp
number of sequenced bases = 11,039,009,848 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 27,659,529
duplication rate = 35.3%
>>>>>>> Insert size
mean insert size = 18,585.1015
std insert size = 1,414,329.9368
median insert size = 237
>>>>>>> Mapping quality
mean mapping quality = 55.7306
>>>>>>> ACTG content
number of A's = 2,778,662,101 bp (25.17%)
number of C's = 2,739,041,377 bp (24.81%)
number of T's = 2,802,844,491 bp (25.39%)
number of G's = 2,717,465,835 bp (24.62%)
number of N's = 996,044 bp (0.01%)
GC percentage = 49.43%
>>>>>>> Mismatches and indels
general error rate = 0.0062
number of mismatches = 67,504,091
number of insertions = 531,226
mapped reads with insertion percentage = 0.69%
number of deletions = 648,630
mapped reads with deletion percentage = 0.85%
homopolymer indels = 46.18%
>>>>>>> Coverage
mean coverageData = 3.5665X
std coverageData = 22.2598X
There is a 23.26% of reference with a coverageData >= 1X
There is a 14.33% of reference with a coverageData >= 2X
There is a 9.06% of reference with a coverageData >= 3X
There is a 6.98% of reference with a coverageData >= 4X
There is a 5.58% of reference with a coverageData >= 5X
There is a 4.86% of reference with a coverageData >= 6X
There is a 4.38% of reference with a coverageData >= 7X
There is a 4.08% of reference with a coverageData >= 8X
There is a 3.87% of reference with a coverageData >= 9X
There is a 3.72% of reference with a coverageData >= 10X
There is a 3.6% of reference with a coverageData >= 11X
There is a 3.5% of reference with a coverageData >= 12X
There is a 3.42% of reference with a coverageData >= 13X
There is a 3.34% of reference with a coverageData >= 14X
There is a 3.28% of reference with a coverageData >= 15X
There is a 3.22% of reference with a coverageData >= 16X
There is a 3.16% of reference with a coverageData >= 17X
There is a 3.11% of reference with a coverageData >= 18X
There is a 3.06% of reference with a coverageData >= 19X
There is a 3.01% of reference with a coverageData >= 20X
There is a 2.96% of reference with a coverageData >= 21X
There is a 2.92% of reference with a coverageData >= 22X
There is a 2.88% of reference with a coverageData >= 23X
There is a 2.84% of reference with a coverageData >= 24X
There is a 2.8% of reference with a coverageData >= 25X
There is a 2.76% of reference with a coverageData >= 26X
There is a 2.73% of reference with a coverageData >= 27X
There is a 2.69% of reference with a coverageData >= 28X
There is a 2.65% of reference with a coverageData >= 29X
There is a 2.62% of reference with a coverageData >= 30X
There is a 2.59% of reference with a coverageData >= 31X
There is a 2.56% of reference with a coverageData >= 32X
There is a 2.52% of reference with a coverageData >= 33X
There is a 2.49% of reference with a coverageData >= 34X
There is a 2.46% of reference with a coverageData >= 35X
There is a 2.43% of reference with a coverageData >= 36X
There is a 2.4% of reference with a coverageData >= 37X
There is a 2.38% of reference with a coverageData >= 38X
There is a 2.35% of reference with a coverageData >= 39X
There is a 2.32% of reference with a coverageData >= 40X
There is a 2.29% of reference with a coverageData >= 41X
There is a 2.27% of reference with a coverageData >= 42X
There is a 2.24% of reference with a coverageData >= 43X
There is a 2.22% of reference with a coverageData >= 44X
There is a 2.19% of reference with a coverageData >= 45X
There is a 2.16% of reference with a coverageData >= 46X
There is a 2.14% of reference with a coverageData >= 47X
There is a 2.12% of reference with a coverageData >= 48X
There is a 2.09% of reference with a coverageData >= 49X
There is a 2.07% of reference with a coverageData >= 50X
There is a 2.04% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 1124767908 4.512598217358103 25.992454735344957
chr2 243199373 822020090 3.3800255315625343 22.09557943198449
chr3 198022430 648908799 3.2769459449618914 21.020602422078955
chr4 191154276 393516047 2.0586306267090775 15.38443478257897
chr5 180915260 539606672 2.9826487384204072 20.56458393668071
chr6 171115067 566495326 3.310610432686211 21.33105064047004
chr7 159138663 534508579 3.3587600204986012 21.454032881368672
chr8 146364022 420780400 2.874889568148107 19.872209209344486
chr9 141213431 451395252 3.1965461698894635 20.819995700367162
chr10 135534747 433099390 3.195486025439661 19.813284582519042
chr11 135006516 646173940 4.786242613652811 27.020054427188732
chr12 133851895 585214541 4.3721050120358775 24.246541077371297
chr13 115169878 213925034 1.857473826619839 15.26489192047698
chr14 107349540 374569244 3.489248710334483 22.035287196832197
chr15 102531392 396727727 3.8693293757291425 22.420989532400487
chr16 90354753 465560576 5.152585343241434 27.063630678112656
chr17 81195210 602211955 7.416840907240711 31.420952334555977
chr18 78077248 210941399 2.701701256171324 21.86831781564927
chr19 59128983 630518617 10.663444304462331 38.162839701401595
chr20 63025520 297224804 4.715943700266178 26.48159238229463
chr21 48129895 117127469 2.433570008827154 21.243246808870108
chr22 51304566 196149450 3.823235733053467 20.012299951320273
chrMT 16571 884965 53.404441494176574 19.90080145755127
chrX 155270560 363604787 2.341749698075411 16.596262595087403
chrY 59373566 4883532 0.08225094649022766 2.2401044129989303