BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3212680.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,937,917
number of mapped reads = 2,684,143 (91.36%)
number of supplementary alignments = 26,525 (0.9%)
number of secondary alignments = 0
number of mapped bases = 181,112,573 bp
number of sequenced bases = 181,047,493 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 124,301
duplication rate = 3.7%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8835
>>>>>>> ACTG content
number of A's = 50,223,341 bp (27.74%)
number of C's = 34,426,385 bp (19.02%)
number of T's = 56,210,258 bp (31.05%)
number of G's = 40,185,495 bp (22.2%)
number of N's = 2,014 bp (0%)
GC percentage = 41.21%
>>>>>>> Mismatches and indels
general error rate = 0.0092
number of mismatches = 1,635,629
number of insertions = 13,870
mapped reads with insertion percentage = 0.51%
number of deletions = 39,992
mapped reads with deletion percentage = 1.47%
homopolymer indels = 46.96%
>>>>>>> Coverage
mean coverageData = 0.0585X
std coverageData = 0.4472X
There is a 4.84% of reference with a coverageData >= 1X
There is a 0.74% of reference with a coverageData >= 2X
There is a 0.14% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 15366729 0.06165171801116596 0.8217993408688463
chr2 243199373 14117298 0.05804824998459186 0.4877711053683397
chr3 198022430 12895515 0.06512148649019205 0.2975589458384308
chr4 191154276 12214391 0.06389807884810278 0.3147475207340001
chr5 180915260 10927468 0.06040102974176971 0.2876209007023662
chr6 171115067 11708530 0.0684248921224453 0.4293569929552207
chr7 159138663 9038131 0.05679406141548393 0.5329243407455209
chr8 146364022 9522438 0.06505996398486508 0.4601643687137952
chr9 141213431 7382632 0.05227995628829385 0.4160439359392904
chr10 135534747 7731210 0.057042272709595276 0.4616242325060789
chr11 135006516 8003875 0.059285101468732074 0.39465736860664224
chr12 133851895 8928145 0.06670167052920693 0.30599484831265616
chr13 115169878 5875185 0.051013208505786556 0.2624997096551685
chr14 107349540 5436642 0.050644297125073845 0.2956370415652579
chr15 102531392 4761165 0.046436168544361514 0.2517439070470456
chr16 90354753 5635255 0.06236810807285368 0.3416620404653466
chr17 81195210 4307594 0.053052316756123916 0.3210240933926752
chr18 78077248 4101603 0.05253262768687749 0.7615450057956694
chr19 59128983 2837550 0.04798915618081914 0.616474006660883
chr20 63025520 3668626 0.058208579635677736 0.2911567396106877
chr21 48129895 2301334 0.04781506379766671 0.29408427238876195
chr22 51304566 2040510 0.039772483408201914 0.23126684377338855
chrMT 16571 138527 8.359604127692958 4.7613944160629496
chrX 155270560 11692508 0.07530408855355451 0.36292581487674913
chrY 59373566 479712 0.008079555134013679 0.1749937867734332