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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,920,950	C→T	80 (TAG→TAA)	atpE ←	F0 sector of membrane‑bound ATP synthase, subunit c

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,920,950	0	C	T	98.3%	184.7 / NA	59	80 (TAG→TAA)	atpE	F0 sector of membrane‑bound ATP synthase, subunit c
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (33/25); minor base G (1/0); total (34/25)
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

CATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTGCGCCTTCC  >  NC_000913/3920823‑3921082

cATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGc                                                                                                                           >  2:239568/1‑139 (MQ=255)

  tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGa                                                                                                                         <  1:691401/139‑1 (MQ=255)

  tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGa                                                                                                                         >  2:119945/1‑139 (MQ=255)

  tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGa                                                                                                                         <  2:319854/139‑1 (MQ=255)

  tGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGAGTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTAGTACGCGACAGCGa                                                                                                                         >  2:725090/1‑139 (MQ=255)

    cagaacagaaCGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAAc                                                                                                                       >  2:308237/1‑139 (MQ=255)

                 acAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagac                                                                                                          >  1:55524/1‑139 (MQ=255)

                 acAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATGCACAGCACAATGCCTCTATTTAGGTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagac                                                                                                          >  1:694900/1‑139 (MQ=255)

                  cAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagacc                                                                                                         <  1:791632/139‑1 (MQ=255)

                          aCGCTATGGCCTGGCCGAGTATTTTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCATGAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTa                                                                                                 <  1:725090/139‑1 (MQ=255)

                          aCGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAca                                                                                                             >  2:494774/1‑127 (MQ=255)

                          aCGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAca                                                                                                             <  1:494774/127‑1 (MQ=255)

                           cgcgATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTAc                                                                                                >  2:454333/1‑139 (MQ=255)

                               aTGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCg                                                                                            >  2:16211/1‑139 (MQ=255)

                                tggcctggccGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagacc                                                                                                         >  2:567716/1‑125 (MQ=255)

                                tggcctggccGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAACAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagacc                                                                                                         <  1:567716/125‑1 (MQ=255)

                                         cGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGa                                                                                  <  1:454333/139‑1 (MQ=255)

                                         cGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGa                                                                                  <  1:119945/139‑1 (MQ=255)

                                                 gttgCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCggg                                                                                   <  2:689501/130‑1 (MQ=255)

                                                 gttgCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTAAAGCGATCATCggg                                                                                   >  1:689501/1‑130 (MQ=255)

                                                       ttAAGATTCACAGCACATTGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGa                                                                    >  2:560244/1‑139 (MQ=255)

                                                       ttAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagaccca                                                                                                       <  2:663749/104‑1 (MQ=255)

                                                       ttAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagaccca                                                                                                       >  1:663749/1‑104 (MQ=255)

                                                                  aGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGAt                                                         <  2:416620/139‑1 (MQ=255)

                                                                  aGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGAt                                                         >  1:259794/1‑139 (MQ=255)

                                                                         tGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAg                                                                                              <  1:83657/95‑1 (MQ=255)

                                                                         tGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAg                                                                                              >  2:83657/1‑95 (MQ=255)

                                                                         tGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAAc                                                  >  2:294757/1‑139 (MQ=255)

                                                                          gCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACt                                                 <  1:239568/139‑1 (MQ=255)

                                                                            ctctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGa                                               <  1:294757/139‑1 (MQ=255)

                                                                                      ttAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACgcagca                                     >  1:155551/1‑139 (MQ=255)

                                                                                      ttAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACgcagca                                     <  1:186340/139‑1 (MQ=255)

                                                                                      ttAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACgcagca                                     <  1:191934/139‑1 (MQ=255)

                                                                                        aaCGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCaga                                   <  1:554945/139‑1 (MQ=255)

                                                                                           gTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGa                                >  1:103671/1‑139 (MQ=255)

                                                                                            ttCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGaa                               <  1:16211/139‑1 (MQ=255)

                                                                                              cTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatc                             <  2:55524/139‑1 (MQ=255)

                                                                                              atGATATTGCTATTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatc                             <  2:694900/138‑1 (MQ=255)

                                                                                                     tGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatcagatcag                      >  1:371848/1‑139 (MQ=255)

                                                                                                      gCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatcagatca                       <  1:389814/137‑1 (MQ=255)

                                                                                                      gCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatcagatca                       >  2:389814/1‑137 (MQ=255)

                                                                                                      gCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAgg                     >  1:787337/1‑139 (MQ=255)

                                                                                                       ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATaa                                                             <  2:463471/98‑1 (MQ=255)

                                                                                                       ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATaa                                                             >  1:463471/1‑98 (MQ=255)

                                                                                                       ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGt                    >  2:333248/1‑139 (MQ=255)

                                                                                                       ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGt                    >  2:30160/1‑139 (MQ=255)

                                                                                                       ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGt                    >  2:296160/1‑139 (MQ=255)

                                                                                                       ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGt                    >  2:284113/1‑139 (MQ=255)

                                                                                                       ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGt                    >  1:476708/1‑139 (MQ=255)

                                                                                                         ctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTg                  >  1:798256/1‑139 (MQ=255)

                                                                                                          tttAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccacc                                                                       >  2:725302/1‑85 (MQ=255)

                                                                                                          tttAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccacc                                                                       <  1:725302/85‑1 (MQ=255)

                                                                                                           ttAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGAc                >  2:271782/1‑139 (MQ=255)

                                                                                                            taaataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGAcg               >  2:116428/1‑139 (MQ=255)

                                                                                                                   aaGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTgcg        <  1:560244/139‑1 (MQ=255)

                                                                                                                    aGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTgcgc       >  1:627131/1‑139 (MQ=255)

                                                                                                                         cGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTGCGCCTTcc  >  2:641109/1‑139 (MQ=255)

                                                                                                                          gCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGa                                                    >  1:301537/1‑88 (MQ=255)

                                                                                                                          gCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGa                                                    <  2:301537/88‑1 (MQ=255)

CATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTGCGCCTTCC  >  NC_000913/3920823‑3921082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A