BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3084812.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 = 2,330,291
number of mapped reads = 2,106,410 (90.39%)
number of supplementary alignments = 20,694 (0.89%)
number of secondary alignments = 0
number of mapped bases = 140,508,388 bp
number of sequenced bases = 140,455,144 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 99,279
duplication rate = 4.07%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.1524
>>>>>>> ACTG content
number of A's = 38,040,353 bp (27.08%)
number of C's = 26,342,899 bp (18.76%)
number of T's = 44,023,207 bp (31.34%)
number of G's = 32,028,501 bp (22.8%)
number of N's = 20,184 bp (0.01%)
GC percentage = 41.56%
>>>>>>> Mismatches and indels
general error rate = 0.0079
number of mismatches = 1,087,699
number of insertions = 10,922
mapped reads with insertion percentage = 0.52%
number of deletions = 32,146
mapped reads with deletion percentage = 1.51%
homopolymer indels = 47.57%
>>>>>>> Coverage
mean coverageData = 0.0454X
std coverageData = 0.3099X
There is a 3.75% of reference with a coverageData >= 1X
There is a 0.59% of reference with a coverageData >= 2X
There is a 0.12% 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% 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 11995773 0.04812735451519697 0.35818722385554363
chr2 243199373 10559433 0.043418833156284496 0.48194646671979546
chr3 198022430 10282887 0.05192789018900536 0.2671108003146835
chr4 191154276 8502584 0.044480218689954915 0.2510734431575268
chr5 180915260 7841496 0.04334347472955018 0.24453221127520205
chr6 171115067 11056513 0.06461449125342071 0.31930064931336366
chr7 159138663 7330842 0.046065750847737105 0.3146032572694054
chr8 146364022 7006802 0.04787243411499036 0.29804871028669716
chr9 141213431 9615316 0.06809066199942412 0.3607850310295194
chr10 135534747 4204385 0.03102071677604563 0.2164844173127398
chr11 135006516 8363104 0.06194592859503167 0.4194559083946825
chr12 133851895 5919228 0.04422222038769044 0.24938260882376453
chr13 115169878 3778085 0.03280445430358101 0.21264918141053382
chr14 107349540 2549374 0.023748345824304417 0.18792678766992896
chr15 102531392 3485989 0.03399923605835762 0.23090719774932064
chr16 90354753 2134876 0.023627711095618845 0.1915899140680142
chr17 81195210 3091294 0.03807236904738592 0.26714979278257844
chr18 78077248 5153252 0.0660019676923039 0.45813288685731246
chr19 59128983 2558583 0.04327121608027657 0.29506882454490574
chr20 63025520 2468931 0.039173512570780854 0.2363735941425087
chr21 48129895 1147759 0.023847112070367077 0.19031695614092367
chr22 51304566 1215436 0.023690600949630877 0.17802167420522447
chrMT 16571 22859 1.3794580894333475 1.457803090815461
chrX 155270560 9920830 0.06389382507540387 0.31848838135869284
chrY 59373566 302757 0.005099188416609506 0.09342684474791826