BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1819144.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,396,990
number of mapped reads = 1,264,580 (90.52%)
number of supplementary alignments = 5,557 (0.4%)
number of secondary alignments = 0
number of mapped bases = 73,327,087 bp
number of sequenced bases = 73,304,436 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 71,475
duplication rate = 4.44%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6494
>>>>>>> ACTG content
number of A's = 18,574,538 bp (25.34%)
number of C's = 12,462,407 bp (17%)
number of T's = 23,641,480 bp (32.25%)
number of G's = 18,624,997 bp (25.41%)
number of N's = 1,014 bp (0%)
GC percentage = 42.41%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 378,780
number of insertions = 5,090
mapped reads with insertion percentage = 0.4%
number of deletions = 13,541
mapped reads with deletion percentage = 1.06%
homopolymer indels = 43.94%
>>>>>>> Coverage
mean coverageData = 0.0237X
std coverageData = 0.2479X
There is a 2.05% of reference with a coverageData >= 1X
There is a 0.23% of reference with a coverageData >= 2X
There is a 0.04% 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 7252590 0.029097580462999127 0.45656718419316844
chr2 243199373 5763174 0.023697322607817744 0.3044866564634024
chr3 198022430 3836709 0.01937512331305095 0.15666740122296877
chr4 191154276 4216067 0.0220558341054322 0.2025283965431195
chr5 180915260 3976448 0.021979616313184416 0.1674500928314043
chr6 171115067 3194402 0.018668151531039637 0.18367815792145037
chr7 159138663 3684166 0.02315066578132556 0.2830626472079833
chr8 146364022 6691801 0.045720259040162206 0.28687324325944724
chr9 141213431 3172355 0.02246496652290815 0.20251441443171006
chr10 135534747 3928425 0.028984633733812923 0.2704008900680095
chr11 135006516 2506998 0.018569459269654805 0.20928508355699624
chr12 133851895 3382961 0.02527391188596919 0.1799009734792451
chr13 115169878 1637680 0.0142196903256249 0.13478670996306527
chr14 107349540 1673180 0.015586280108885422 0.14342030826945534
chr15 102531392 1946662 0.018986009670092063 0.15525105297917915
chr16 90354753 2269333 0.02511581211449939 0.18782424060994188
chr17 81195210 2558745 0.03151349691687478 0.20831058933233076
chr18 78077248 1749311 0.022404875233307402 0.34576983193361777
chr19 59128983 1505648 0.025463789898094474 0.3055216720130539
chr20 63025520 2064270 0.03275292294296025 0.20879073971386566
chr21 48129895 1016542 0.021120802362024682 0.1826073746441875
chr22 51304566 611915 0.011927106059137115 0.12459403776974336
chrMT 16571 8758 0.5285136684569428 0.9625599801707018
chrX 155270560 4390442 0.028276075000953176 0.20123597805093885
chrY 59373566 288505 0.004859148935066491 0.1614904552945395