Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A11 F50 I0 R1	804	34.5	1706502	92.5%	1578514	135.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,397,705	A→T	24.1%	L223F (TTA→TTT)	hsdS →	type I restriction modification system specificity protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,397,705	0	A	T	24.1%	50.4 / 16.3	29	L223F (TTA→TTT)	hsdS	type I restriction modification system specificity protein
Reads supporting (aligned to +/- strand): ref base A (13/9); new base T (4/3); total (17/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.54e-01

CCGGCGCCAACATTGCCAGAGCTATTTGCCGTGTAGTCCCCAGTGTGCATGTCTCGAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGCCGAGTCCGCCCACGTC  >  NC_002947/5397563‑5397846

ccGGCGCCAACATTGCCAGAGCTATTTGCCGTGTAGTCCCCAGTGTGCATGTCTCGAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTg                                                                                                                                        <  1:341531/150‑1 (MQ=255)

   acgcCAACATTGCCAGAGCTATTTGCCGTGTAGTCCCCAGTGTGCATGTCTCGAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGcc                                                                                                                                     >  2:33885/2‑150 (MQ=255)

                 agagCTATGTGCCGTGTAGTCCCCAGTGTGCATGTCTCGAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATGCGTAGTGcc                                                                                                                       >  2:816609/1‑150 (MQ=255)

                                      cccAGTGTGCATGTCTCGAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTTAATGTTGGct                                                                                                                                     >  1:164389/1‑114 (MQ=255)

                                      cccAGTGTGCATGTCTCGAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTTAATGTTGGct                                                                                                                                     <  2:164389/115‑2 (MQ=255)

                                                       gAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCAt                                                                                 >  1:716233/1‑150 (MQ=255)

                                                                              tACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTc                                                                                                       <  2:324899/105‑1 (MQ=255)

                                                                              tACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTc                                                                                                       >  1:324899/1‑105 (MQ=255)

                                                                              tACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACGACACCGCATCGTTGCCAAAGTCGAAGAACTaa                                                          >  2:726102/1‑150 (MQ=255)

                                                                              tACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTaa                                                          >  1:350542/1‑150 (MQ=255)

                                                                                 aaaGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATgg                                                       >  2:576451/1‑150 (MQ=255)

                                                                                         cTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGc                                               <  1:576451/150‑1 (MQ=255)

                                                                                           tATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGa                                             <  1:33885/150‑1 (MQ=255)

                                                                                              gCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCACCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGTCAAAGTCGAAGAACTAATGGCCCTATGCGACCg                                          <  1:416075/150‑1 (MQ=255)

                                                                                                gAAAGCCGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCt                                        >  2:444775/1‑150 (MQ=255)

                                                                                                  aaGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACAGTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAAATAATGGCCCTATGCGACCGCTTg                                      >  1:272568/1‑150 (MQ=255)

                                                                                                   aGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGaacaa                                                                                         <  1:326962/98‑1 (MQ=255)

                                                                                                   aGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGaacaa                                                                                         >  2:326962/1‑98 (MQ=255)

                                                                                                           ttGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCcag                             <  2:350542/150‑1 (MQ=255)

                                                                                                                      tCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGc                  >  2:845951/1‑150 (MQ=255)

                                                                                                                            ccTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGATCAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCcagca                           <  2:241788/135‑1 (MQ=255)

                                                                                                                            ccTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGATCAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCcagca                           >  1:241788/1‑135 (MQ=255)

                                                                                                                                gCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGCCGAGTCCGcc        <  1:845951/150‑1 (MQ=255)

                                                                                                                                     gCCAACATTTAATGTTGGCTTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGCCGAGTCCGc         <  2:86563/144‑1 (MQ=255)

                                                                                                                                     gCCAACATTTAATGTTGGCTTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGCCGAGTCCGc         >  1:86563/1‑144 (MQ=255)

                                                                                                                                     gCCAACATTTAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGAc                                            <  2:278078/109‑1 (MQ=255)

                                                                                                                                     gCCAACATTTAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGAc                                            >  1:278078/1‑109 (MQ=255)

                                                                                                                                     gCCAACATTTAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGCCGAGTCCGCCCACGt   >  1:380846/1‑150 (MQ=255)

                                                                                                                                      ccAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGCCGAGTCCGCCCACGTc  >  2:840745/1‑150 (MQ=255)

CCGGCGCCAACATTGCCAGAGCTATTTGCCGTGTAGTCCCCAGTGTGCATGTCTCGAAGGACTACATAATTTGGTTGCTACAAAGTGACCTTATGCGAAAGCAGTTCTTGGGAGATACTCGAACCCTCGCCCAGCCAACATTAAATGTTGGCCTGATTCGTAGTGCCGCGGCACCTCTGCCTCCCCTCGCCGAACAACACCGCATCGTTGCCAAAGTCGAAGAACTAATGGCCCTATGCGACCGCTTGGAAGCCCAGCAGGCCGACGCCGAGTCCGCCCACGTC  >  NC_002947/5397563‑5397846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A