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
A7 F184 I1 R1	31	33.8	680504	95.8%	651922	149.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,709,576	C→T	G451S (GGT→AGT)	oatA ←	possible acetyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,709,576	0	C	T	96.8%	100.0 / NA	31	G451S (GGT→AGT)	oatA	possible acetyltransferase
Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (18/12); total (19/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCATGTTGT  >  CP000730/2709432‑2709715

tttGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAAtt                                                                                                                                         <  1:214458/149‑1 (MQ=255)

        tttttAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAgtgg                                                                                                                                 >  1:247853/1‑149 (MQ=255)

                    tCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTATAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACttttt                                                                                                                     >  2:22806/1‑149 (MQ=255)

                       ttATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCACCTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGCGTAACTAATTAATACTGGTGATGACTTTTTAat                                                                                                                  >  2:117987/1‑149 (MQ=255)

                            ttGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCct                                                                                                             <  1:338698/149‑1 (MQ=255)

                               cggtttCACAATTGGTGTAGCATCAACGCGTTGCCGTCCAACTTTAACATCAATTTGTGCATTTGGTATTTTCTTAGTAAAAACATTATCAATATCCATCATGAACGAGATACCAATTAAAAGTTGTTATGACTTTTTatttttccttt                                                                                                          >  2:146200/4‑139 (MQ=255)

                               cGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCtt                                                                                                          >  2:134713/1‑149 (MQ=255)

                               cGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGGGATGACTTTTTAATATACTCtt                                                                                                          >  2:199451/1‑149 (MQ=255)

                                gATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCttt                                                                                                         >  1:72560/1‑149 (MQ=255)

                                            ggTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGt                                                                                             >  2:40908/1‑149 (MQ=255)

                                               gtAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTg                                                                                          <  2:16725/149‑1 (MQ=255)

                                                       aaCGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCct                                                                                  <  2:77885/149‑1 (MQ=255)

                                                                   tCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCtt                                                                      >  1:10157/1‑149 (MQ=255)

                                                                           tACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACg                                                              >  1:313759/1‑149 (MQ=255)

                                                                           tACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACg                                                              <  2:12209/149‑1 (MQ=255)

                                                                                 cAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACtttt                                                        >  1:339228/1‑149 (MQ=255)

                                                                                                  aTTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTaaa                                       >  2:224679/1‑149 (MQ=255)

                                                                                                           gTAAAGACATTACCAATATCGACCATGATCGAGTAACTAATTAATAGTGGTGATGACTTTTTAATAGTCTCTTTGCTATTCGCTGTCTGATTATCCGCTTGCTTATCTTTTTTATTGACTTTTTTTTTCGTTGTTTTATATTccttttt                              >  2:218274/1‑144 (MQ=255)

                                                                                                            tAAAGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtcttc                             >  2:294590/1‑149 (MQ=255)

                                                                                                             aaaGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtcttct                            <  1:35244/149‑1 (MQ=255)

                                                                                                              aaGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtcttctt                           >  2:188404/1‑149 (MQ=255)

                                                                                                               aGACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtcttcttc                          <  1:289814/149‑1 (MQ=255)

                                                                                                                gACATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGtcttcttct                         >  1:91771/1‑149 (MQ=255)

                                                                                                                 aCATTACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTtctc                        >  2:74709/1‑149 (MQ=255)

                                                                                                                    ttACCAATATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCtcttt                     <  2:99159/149‑1 (MQ=255)

                                                                                                                         aaTATCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTtcttct                >  2:59415/1‑149 (MQ=255)

                                                                                                                             tCCACCATGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGc            <  1:134713/149‑1 (MQ=255)

                                                                                                                                 ccaTGACCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCa        <  2:10157/149‑1 (MQ=255)

                                                                                                                                      aCCGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCAtgttg   >  1:162723/1‑149 (MQ=255)

                                                                                                                                       ccGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCAtgttgt  <  1:9744/149‑1 (MQ=255)

                                                                                                                                       ccGAGTCACTAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCAtgttgt  <  2:10877/149‑1 (MQ=255)

TTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCACCAATTAATAGTGGTGATGACTTTTTAATATCCTCTTTGCTATTCGCTGTCTGCTTATCCTCTTGCTTATCTTTTTTAACGACTTTTTTCTTCGTTGTTTTAAATTCCGTCTTCTTCTCTTTCTTCTCGGCTTCATGTTGT  >  CP000730/2709432‑2709715

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

GATK/CNVnator alignment

N/A