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 F1 I1 R1	57	49.8	2216334	94.8%	2101084	113.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,282	G→A	G582R (GGA→AGA)	flu →	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,073,282	0	G	A	100.0%	102.4 / NA	30	G582R (GGA→AGA)	flu	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (13/17); total (13/17)

CTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGA  >  NC_000913/2073150‑2073412

cTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCcagacaga                                                                                                                              <  2:570157/139‑1 (MQ=255)

   aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTc                                                                                                                           >  1:488353/1‑139 (MQ=255)

   aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTc                                                                                                                           >  1:959559/1‑139 (MQ=255)

     gCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCAt                                                                                                                         <  1:517890/139‑1 (MQ=255)

      cTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCAtt                                                                                                                        <  1:534626/139‑1 (MQ=255)

           cGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCAcc                                                                                                                   <  2:839160/139‑1 (MQ=255)

                    tgtgCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGc                                                                                                          >  1:198283/1‑139 (MQ=255)

                                          cccACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCaa                                                                                    >  1:111328/1‑139 (MQ=255)

                                                 aTGTCACTCTCGCCTCCGGTGCCGCCTGGAATATCCCCGATAACGCCACGGTGCAGTGGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCCCCCGCACAGGGAAGTTCGTACCGGGAACCCTGaa                                                                             <  2:323846/139‑1 (MQ=255)

                                                      aCTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGa                                                                        <  2:509588/139‑1 (MQ=255)

                                                            gCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAAcc                                                                  >  2:944981/1‑139 (MQ=255)

                                                                        aCCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGa                                                      <  2:198283/139‑1 (MQ=255)

                                                                                        aTAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCt                                      >  2:1057499/1‑139 (MQ=255)

                                                                                        aTAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCt                                      <  1:944981/139‑1 (MQ=255)

                                                                                             gCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCgtg                                 <  1:503632/139‑1 (MQ=255)

                                                                                             gCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCgtg                                 <  1:1057499/139‑1 (MQ=255)

                                                                                                  ggTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGc                            >  1:971534/1‑139 (MQ=255)

                                                                                                         tCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGata                     <  2:959559/139‑1 (MQ=255)

                                                                                                              ggtggATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGca                >  2:139289/1‑139 (MQ=255)

                                                                                                              ggtggATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGca                <  2:188892/139‑1 (MQ=255)

                                                                                                                   aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc                                                                                                              <  1:595387/40‑1 (MQ=255)

                                                                                                                   aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc                                                                                                              >  2:595387/1‑40 (MQ=255)

                                                                                                                   aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               <  2:199918/87‑1 (MQ=255)

                                                                                                                   aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               >  1:199918/1‑87 (MQ=255)

                                                                                                                   aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGaa           <  1:1068188/139‑1 (MQ=255)

                                                                                                                     gACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGata                     <  2:1055111/127‑1 (MQ=255)

                                                                                                                     gACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGata                     >  1:1055111/1‑127 (MQ=255)

                                                                                                                       ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               <  2:1035949/83‑1 (MQ=255)

                                                                                                                       ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               >  1:1035949/1‑83 (MQ=255)

                                                                                                                          cAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCt    >  2:748485/1‑139 (MQ=255)

                                                                                                                            gCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGa  <  2:971534/139‑1 (MQ=255)

CTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGA  >  NC_000913/2073150‑2073412

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A