BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524434.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 = 516,740
number of mapped reads = 474,171 (91.76%)
number of supplementary alignments = 2,105 (0.41%)
number of secondary alignments = 0
number of mapped bases = 27,769,349 bp
number of sequenced bases = 27,761,304 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,400
duplication rate = 1.7%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6228
>>>>>>> ACTG content
number of A's = 6,725,676 bp (24.23%)
number of C's = 5,113,790 bp (18.42%)
number of T's = 9,040,856 bp (32.57%)
number of G's = 6,878,016 bp (24.78%)
number of N's = 2,966 bp (0.01%)
GC percentage = 43.2%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 139,718
number of insertions = 2,215
mapped reads with insertion percentage = 0.47%
number of deletions = 4,901
mapped reads with deletion percentage = 1.03%
homopolymer indels = 41.64%
>>>>>>> Coverage
mean coverageData = 0.009X
std coverageData = 0.1198X
There is a 0.85% of reference with a coverageData >= 1X
There is a 0.03% of reference with a coverageData >= 2X
There is a 0% 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 2341038 0.00939230558627174 0.19648353520196643
chr2 243199373 2264437 0.009311031406318634 0.14225500618210754
chr3 198022430 1891166 0.00955026155370379 0.1016402521441881
chr4 191154276 1812355 0.009481111476679705 0.10929641736854852
chr5 180915260 1675225 0.009259721927271364 0.0997077488152836
chr6 171115067 1115070 0.006516492203459792 0.08571031814776436
chr7 159138663 1575603 0.009900818382519652 0.14283261982524087
chr8 146364022 1453390 0.009929967625513871 0.11040243121684015
chr9 141213431 1026906 0.007272013665612303 0.09445719838700237
chr10 135534747 1410806 0.010409183115234649 0.12775559090789212
chr11 135006516 1142408 0.008461873055075356 0.10287184925037589
chr12 133851895 1275762 0.009531146346489902 0.10222002841660116
chr13 115169878 885367 0.007687487521693823 0.09106198172937771
chr14 107349540 751853 0.007003784087011458 0.0880995959851072
chr15 102531392 865379 0.008440137046027816 0.09580166569091658
chr16 90354753 868492 0.009612023398481316 0.10342186591192527
chr17 81195210 773024 0.009520561619336905 0.10307158057069966
chr18 78077248 742547 0.00951041460887556 0.13005410636534162
chr19 59128983 816787 0.013813648714370751 0.15841170527815732
chr20 63025520 774027 0.012281168009403175 0.11649285731032252
chr21 48129895 376750 0.007827775232004973 0.09703716832713875
chr22 51304566 202014 0.003937544272375289 0.06545904501672961
chrMT 16571 43604 2.631343914066743 2.3314158469087136
chrX 155270560 1589555 0.010237323804332257 0.10766012187748515
chrY 59373566 95784 0.0016132431728961673 0.06256931331097469