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
A13 F1 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,781,688	G→A	158 (TAG→TAA)	trmL →	tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,688	0	G	A	97.5%	119.4 / ‑4.4	40	158 (TAG→TAA)	trmL	tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (15/24); total (15/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

CTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCTG  >  NC_000913/3781554‑3781823

ctgcccGCTGCACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTAc                                                                                                                                     >  2:516768/1‑139 (MQ=255)

 tgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAACCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACt                                                                                                                                    <  1:529094/139‑1 (MQ=255)

        tGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGcc                                                                                                                             >  1:487199/1‑139 (MQ=255)

           aCAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGa                                                                                                                          <  2:765483/139‑1 (MQ=255)

           aCAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGa                                                                                                                          >  2:422145/1‑139 (MQ=255)

             aaaaaaTTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                        <  1:146622/139‑1 (MQ=255)

                    tCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACt                                                                                                                                    >  2:660551/1‑120 (MQ=255)

                    tCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACt                                                                                                                                    <  1:660551/120‑1 (MQ=255)

                                  tGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGc                                                                                                   <  2:342131/139‑1 (MQ=255)

                                      ggACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGa                                                                                               >  2:466564/1‑139 (MQ=255)

                                         cAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGATAGATTAGTTACTGTAGGCCGGAGAGATGATTACATCGCATCCGGTACGATca                                                                                            <  2:445789/139‑1 (MQ=255)

                                         cAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATca                                                                                            <  1:466564/139‑1 (MQ=255)

                                           gCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTCCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                          <  2:546051/139‑1 (MQ=255)

                                           gCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                          <  2:531389/139‑1 (MQ=255)

                                           gCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                          <  1:422145/139‑1 (MQ=255)

                                           gCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                          <  1:602053/139‑1 (MQ=255)

                                             cGCAGCATGAAACTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAgg                                                                                        <  1:500628/139‑1 (MQ=255)

                                                             ccAATGCGGTGTCGGGAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGGTTACGTCGCATCCGGCACGATCACAGGACATGAGatcccatcc                                                                        <  2:13206/139‑1 (MQ=255)

                                                                aTGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGTGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCa                                                                     <  2:464634/139‑1 (MQ=255)

                                                                      tgtCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACAt                                                                                                             <  1:762142/93‑1 (MQ=255)

                                                                      tgtCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACAt                                                                                                             >  2:762142/1‑93 (MQ=255)

                                                                           gTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                          <  2:487199/139‑1 (MQ=255)

                                                                                      tGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTAGGGTTAATAc                                               <  1:516768/139‑1 (MQ=255)

                                                                                         aGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                        <  2:630584/63‑1 (MQ=255)

                                                                                         aGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                        >  1:630584/1‑63 (MQ=255)

                                                                                           ccTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTg                                          <  2:605580/139‑1 (MQ=255)

                                                                                            cTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGa                                         >  2:724790/1‑139 (MQ=255)

                                                                                                cggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCa                                                               >  1:470673/1‑113 (MQ=255)

                                                                                                cggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCa                                                               <  2:470673/113‑1 (MQ=255)

                                                                                                  gcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCt                                   <  1:602774/139‑1 (MQ=255)

                                                                                                     gTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGt                                >  1:151561/1‑139 (MQ=255)

                                                                                                          ggTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCata                           <  1:88171/139‑1 (MQ=255)

                                                                                                                  ggAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGa                   <  2:151561/139‑1 (MQ=255)

                                                                                                                        gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGt                                                     <  2:604881/99‑1 (MQ=255)

                                                                                                                        gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGt                                                     >  1:604881/1‑99 (MQ=255)

                                                                                                                        gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCtt             >  1:579881/1‑139 (MQ=255)

                                                                                                                        gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCtt             >  1:738422/1‑139 (MQ=255)

                                                                                                                                agaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                                 >  2:252684/1‑47 (MQ=255)

                                                                                                                                agaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                                 <  1:252684/47‑1 (MQ=255)

                                                                                                                                  attaattaCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcccatcc                                                                        >  1:590928/1‑70 (MQ=255)

                                                                                                                                   ttAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCTg  >  2:67292/1‑139 (MQ=255)

CTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCTG  >  NC_000913/3781554‑3781823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A