BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524418.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 709,611
number of mapped reads = 654,417 (92.22%)
number of supplementary alignments = 2,905 (0.41%)
number of secondary alignments = 0
number of mapped bases = 38,415,230 bp
number of sequenced bases = 38,404,696 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 22,554
duplication rate = 2.61%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8552
>>>>>>> ACTG content
number of A's = 8,881,845 bp (23.13%)
number of C's = 7,830,818 bp (20.39%)
number of T's = 12,350,765 bp (32.16%)
number of G's = 9,336,875 bp (24.31%)
number of N's = 4,393 bp (0.01%)
GC percentage = 44.7%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 194,640
number of insertions = 2,891
mapped reads with insertion percentage = 0.44%
number of deletions = 6,395
mapped reads with deletion percentage = 0.97%
homopolymer indels = 40.91%
>>>>>>> Coverage
mean coverageData = 0.0124X
std coverageData = 0.155X
There is a 1.14% of reference with a coverageData >= 1X
There is a 0.07% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% 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 3151746 0.012644887251855634 0.255946347697961
chr2 243199373 3226982 0.013268874669343823 0.19650307561544292
chr3 198022430 2425332 0.01224776405379936 0.11768754627851297
chr4 191154276 2401454 0.01256291018046596 0.147977639741168
chr5 180915260 2172708 0.01200953418744223 0.11620221542837808
chr6 171115067 2088030 0.012202490619952246 0.12158055848245046
chr7 159138663 2119738 0.013320069177657977 0.1829741603150304
chr8 146364022 1919867 0.013117069166082358 0.13511790123909356
chr9 141213431 1615815 0.011442360606619635 0.1293861254140579
chr10 135534747 1909503 0.014088660231165666 0.17738901949861158
chr11 135006516 1743994 0.012917850572486442 0.13644770478445903
chr12 133851895 1715805 0.012818682918161151 0.12083017902037824
chr13 115169878 1127892 0.00979328987393735 0.10515606149830238
chr14 107349540 1145766 0.010673226918345435 0.11057845458714559
chr15 102531392 1144623 0.011163634645670275 0.11213111775016633
chr16 90354753 1211332 0.013406400435846469 0.12756996560300754
chr17 81195210 1183590 0.014577091431871412 0.13314501036783571
chr18 78077248 1018954 0.013050588053513362 0.19307351085046195
chr19 59128983 926607 0.015670944315074722 0.18882179586621897
chr20 63025520 858881 0.013627511522316674 0.12851858600187782
chr21 48129895 528816 0.01098726685358445 0.13792382961233302
chr22 51304566 546770 0.010657336035159132 0.1103189698351483
chrMT 16571 8810 0.5316516806469133 0.7945771750953264
chrX 155270560 2063926 0.013292448999990726 0.12805144139096677
chrY 59373566 158289 0.0026659843877324127 0.10732176028201633