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
A3 F75 I1 R1	13	22.6	534182	93.9%	501596	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,646,189	G→C	A155G (GCA→GGA)	ypdF ←	Aminopeptidase YpdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,646,189	0	G	C	96.5%	89.0 / NA	29	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (13/15); total (13/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTAT  >  USA300TCH1516_ALE/1646052‑1646313

ttttATTTCTTTCAAAACCATATGGTAATGCATCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTGATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGcctcct                                                                                                                            <  1:201411/140‑1 (MQ=255)

ttttATCACTTGCAACACCATGTGGTAATGCACCTCTATGATCATATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGcctcct                                                                                                                            <  2:61487/140‑1 (MQ=255)

       aCTTGCAACACCATGTTGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAAGTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                     <  1:37905/140‑1 (MQ=255)

              acacCATGTGGTAGGGCACCACGATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaa                                                                                                              <  1:99509/140‑1 (MQ=255)

                    tgtgGTAATGCATCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatata                                                                                                        <  1:75437/140‑1 (MQ=255)

                    tgtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCCTGCCTCCTTTTACAACAGTTAAAatata                                                                                                        >  2:223672/1‑140 (MQ=255)

                      tgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCACTCCTGCCTCCTTTTACAACATTTAAAATATAtt                                                                                                      >  1:201648/1‑140 (MQ=255)

                           aTGCACCTCTCTGACCAGATGCTACAATCGAATCGAATGATGGTCCATCTGCTCCTAACTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACATCTAAAATATCTTCatat                                                                                                 >  2:4587/1‑140 (MQ=255)

                           aTGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGATCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCATTTTACAACAGTTACAATATATTAatat                                                                                                 >  2:134971/1‑140 (MQ=255)

                                       gACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTCAAATCTATTCATCTTTTTCATcaaca                                                                                     >  2:79629/1‑140 (MQ=255)

                                               gCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgc                                                                             >  2:74309/1‑140 (MQ=255)

                                                 tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTATTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                           <  1:142893/140‑1 (MQ=255)

                                                 tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATCCTTTTTCAGTCATGCCTCCTTTTACAACATTTACAATACATTCATATGTTTCATCAACAATATTAgctg                                                                           <  2:147946/140‑1 (MQ=255)

                                                 tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTATAATATTCCCTTTCATTCTTCTTCATTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                           <  2:202537/140‑1 (MQ=255)

                                                     aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTCTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATCTATTCATATGTTTCCTCAACAATATTAGCTGCttt                                                                       >  1:54896/1‑140 (MQ=255)

                                                         tATCGAATGATGGTCCATCTGCTCCGAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATACGTTTCATCAACAATATTAGCTGCTTTTTGa                                                                   <  2:73726/140‑1 (MQ=255)

                                                              aaTGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACATCAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTaa                                                              <  1:102333/140‑1 (MQ=255)

                                                                     gTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAtt                                                       <  2:180191/140‑1 (MQ=255)

                                                                               tCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAt                                             >  2:238037/1‑140 (MQ=255)

                                                                                      tgtAGGATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACGACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                      >  2:262055/3‑140 (MQ=255)

                                                                                            aTTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGACTTAAAGCAATTTCGTCAGCATCTTTGCCGTctct                                >  2:194719/1‑140 (MQ=255)

                                                                                               ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAt                             <  1:239930/140‑1 (MQ=255)

                                                                                                      cTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACTTCTCTATTTTTctct                      >  2:126073/1‑140 (MQ=255)

                                                                                                                cTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAACAATTTCATCAGCATCTTTGACATCTCTAATTTTATCTACAGTATTAg            >  1:132310/1‑140 (MQ=255)

                                                                                                                        atttttCTTTCACGCATGCTTTTACAACACTTAAAATACATTCATATGTTTCATCATCCATATCAGCTCCTTCTTCAATTAAAGCAATTTCGTCAGCATATTTAACGTCTCTAATTTTATCTACACTATTACAAATGCtt    <  2:197303/139‑1 (MQ=255)

                                                                                                                         tttttCATTCATGCCTCCTTGTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:160692/140‑1 (MQ=255)

                                                                                                                         tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:98954/140‑1 (MQ=255)

                                                                                                                         tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:90635/140‑1 (MQ=255)

                                                                                                                         tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:68764/140‑1 (MQ=255)

                                                                                                                         tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:260643/140‑1 (MQ=255)

                                                                                                                          ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATAGTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAAAAATGCttct  >  2:8257/1‑138 (MQ=255)

TTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTAT  >  USA300TCH1516_ALE/1646052‑1646313

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A