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
A21 F42 I0 R1	24	30.6	687070	95.0%	652716	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,372,764	Δ1 bp	21.9%	coding (1012/1335 nt)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,372,764	0	A	.	21.9%	72.1 / 19.2	32	coding (1012/1335 nt)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base A (10/15); new base . (5/2); total (15/17)
Fisher's exact test for biased strand distribution p-value = 2.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

TGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCA  >  USA300TCH1516_ALE/2372624‑2372903

tGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTTCCTGCCGGAACGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAaacaaca                                                                                                                                             <  1:162014/141‑1 (MQ=255)

       tCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGtt                                                                                                                                      >  1:254044/1‑141 (MQ=255)

                    aGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCCACCACCACTTAGGCGGTTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCaa                                                                                                                         <  1:323480/141‑1 (MQ=255)

                          tctcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTg                                                                                                                   >  1:172972/1‑141 (MQ=255)

                              tgCATAGTTTGCAGCCATTAATACACCTACCACCCGTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCt                                                                                                               <  2:10258/140‑1 (MQ=255)

                              aGCAAAGTTTGCAGCCATTAATACACCTACCACCACTCAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCt                                                                                                               <  1:244669/141‑1 (MQ=255)

                                 aaaGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAAC‑ACCTGTTACGATACTAGCAAATCCTGTTCTAGCa                                                                                                           >  1:320471/1‑141 (MQ=255)

                                        gCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGTGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACa                                                                                                     <  2:320309/141‑1 (MQ=255)

                                             cATTAATACACCTACCACCCCTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAac                                                                                                <  2:135226/141‑1 (MQ=255)

                                                  aTACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTg                                                                                           <  1:122712/141‑1 (MQ=255)

                                                      cccTTCCAGCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACACCCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGt                                                                                       <  2:158723/140‑1 (MQ=255)

                                                      acCTACCACCACTAAGGCTGGTGTCGTAACTGCAGATGTTTCAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGt                                                                                       <  2:257505/141‑1 (MQ=255)

                                                          accaccACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGAt                                                                                   <  1:124980/141‑1 (MQ=255)

                                                            caccacTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAAC‑ACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCg                                                                                <  2:214378/141‑1 (MQ=255)

                                                                    gggttGGTCTCGTAACTGCACTTGTTACAACAGCGATTAACGGACGAAAGAACAGCGCTAGTAGGTCGCAACACCTTTTCACGATACTAGCAAATCCTGTTCTAGTACCTACAGCAACACCTGAAGTTGATTCGATATaag                                                                         <  2:168960/137‑1 (MQ=255)

                                                                          gtgtCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAAC‑ACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAgttgt                                                                  >  1:310280/1‑141 (MQ=255)

                                                                              cGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAAC‑ACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGACGTTGACTCGATATAAGAAGTCGTTGTa                                                              >  2:102984/1‑141 (MQ=255)

                                                                                       aCTTGCTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTcc                                                      <  1:144209/141‑1 (MQ=255)

                                                                                        tttGTTACAGCAGTGATTAGGCGAGTGAAGAAGTGTGTTTAGAGGAAACAACAACCTGTGGCGATACGGGCAAATGCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCa                                                     <  2:19468/140‑1 (MQ=255)

                                                                                         ttGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCaa                                                    <  1:211512/141‑1 (MQ=255)

                                                                                          tGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAAC‑ACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTCTAGTTGTTCCaaaa                                                  >  1:244376/1‑141 (MQ=255)

                                                                                              acaacaGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACt                                               >  1:245768/1‑141 (MQ=255)

                                                                                                    gCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCt                                         <  1:225435/141‑1 (MQ=255)

                                                                                                      gATTAACGGATTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTAc                                       <  2:243051/141‑1 (MQ=255)

                                                                                                       aTTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATCAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACa                                      >  1:112388/1‑141 (MQ=255)

                                                                                                            cGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGt                                 >  1:240459/1‑141 (MQ=255)

                                                                                                            cGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGt                                 >  2:230162/1‑141 (MQ=255)

                                                                                                               aCTAAAGAACAGCGCTAATAGGAAACAAC‑ACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCt                             >  2:336230/1‑141 (MQ=255)

                                                                                                                cTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCt                             >  1:313676/1‑141 (MQ=255)

                                                                                                                cTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCt                             >  1:258471/1‑141 (MQ=255)

                                                                                                                 aaaaGAACAGCGCTAATAGGAAACAAC‑ACCTGTTACGATACTAGCAATCCACAGTGTACCACATGCGGGAACACCGGAAGTTGATTCGATATAAGAAGTTGTTGTAGTGGTGCCAGAAACTGATCCTACAATCGTAGCTaa                           <  1:130250/140‑1 (MQ=255)

                                                                                                                         aGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACACCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTCTAGTTGTTCCAAAAACTCACCCTACAACCCTAGCTAACGaaacc                    >  2:139487/1‑138 (MQ=255)

                                                                                                                                aTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACa             >  1:141712/1‑141 (MQ=255)

                                                                                                                                           caacCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCa  <  2:134208/141‑1 (MQ=255)

                                                                                                                                           caacCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTAATCATTCAATAGTAGCTAAAGAAACTGAGAACAATGCTCTACCa  >  1:177254/1‑141 (MQ=255)

TGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCA  >  USA300TCH1516_ALE/2372624‑2372903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A