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
A14 F1 I1 R1	71	51.6	2219666	95.9%	2128659	118.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,225	T→C	W563R (TGG→CGG)	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	2,073,225	0	T	C	97.1%	124.0 / ‑2.9	34	coding (1687/3120 nt)	flu	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (18/15); minor base . (0/1); total (18/16)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.97e-01

CGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGA  >  NC_000913/2073091‑2073356

cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGaa                                                                                                                                 <  2:445684/139‑1 (MQ=255)

cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGaa                                                                                                                                 >  1:75945/1‑139 (MQ=255)

         tgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGa                                                                                                                        <  1:564685/139‑1 (MQ=255)

                     ccGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGt                                                                                                            <  1:848642/139‑1 (MQ=255)

                        tCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCa                                                                                                         >  2:900876/1‑139 (MQ=255)

                          accacGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGt                                                                                                       >  2:599672/1‑139 (MQ=255)

                               ggATGTCATTGCTCAGCGCGTTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCggtg                                                                                                  >  1:1072483/1‑139 (MQ=255)

                                  tGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGgtggtg                                                                                               >  1:308410/1‑139 (MQ=255)

                                    tCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             <  2:308410/139‑1 (MQ=255)

                                    tCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             >  1:838087/1‑139 (MQ=255)

                                    tCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                                                                                             <  2:1013018/139‑1 (MQ=255)

                                     cATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAAGGCCACGGTGCAGTCGGTGGTGGAt                                                                                            <  1:750537/139‑1 (MQ=255)

                                                          ccTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACC‑GGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGa                                                                      <  2:1101537/139‑1 (MQ=255)

                                                              aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTc                                                                   >  1:1055155/1‑139 (MQ=255)

                                                              aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTc                                                                   >  2:259251/1‑139 (MQ=255)

                                                                      cGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCAcc                                                           <  2:1055155/139‑1 (MQ=255)

                                                                           gcaCTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCAc                                                      <  1:572679/139‑1 (MQ=255)

                                                                               tgtgCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCTGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGc                                                  <  1:684490/139‑1 (MQ=255)

                                                                               tgtgCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGc                                                  <  2:855700/139‑1 (MQ=255)

                                                                                        cGGTGCCATTGACCCCACGAATGCCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAg                                         >  2:396807/1‑139 (MQ=255)

                                                                                           tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCa                                                                                                                <  1:247690/65‑1 (MQ=255)

                                                                                           tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCa                                                                                                                >  2:247690/1‑65 (MQ=255)

                                                                                           tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTc                                      >  2:939879/1‑139 (MQ=255)

                                                                                           tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTc                                      >  1:322295/1‑139 (MQ=255)

                                                                                           tGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTc                                      >  1:531646/1‑139 (MQ=255)

                                                                                             ccATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGt                                                                                                       <  1:622422/72‑1 (MQ=255)

                                                                                             ccATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGt                                                                                                       >  2:622422/1‑72 (MQ=255)

                                                                                                           aaTGTCACTCTCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGa                      <  1:259251/139‑1 (MQ=255)

                                                                                                                  ctctCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGt                                                                                                            >  2:636406/1‑46 (MQ=255)

                                                                                                                  ctctCGCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGaa               >  2:483136/1‑139 (MQ=255)

                                                                                                                  ctctCGCCTCCGGTGCCACCCGGAATATACCCGATAACGCCACGGt                                                                                                            <  1:636406/46‑1 (MQ=255)

                                                                                                                       gCCTCCGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAAcc          >  1:555487/1‑139 (MQ=255)

                                                                                                                           ccGGTGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGaa      >  1:581290/1‑139 (MQ=255)

                                                                                                                               tGCCACCCGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGa  <  2:343411/139‑1 (MQ=255)

CGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGA  >  NC_000913/2073091‑2073356

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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