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
A11 F1 I1 R1	63	64.8	2934156	93.7%	2749304	111.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,616	A→G	D693G (GAC→GGC)	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	2,073,616	0	A	G	100.0%	199.3 / NA	52	D693G (GAC→GGC)	flu	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (28/24); total (28/24)

TGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAA  >  NC_000913/2073482‑2073750

tGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGt                                                                                                                                    >  2:985133/1‑139 (MQ=255)

 gCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtg                                                                                                                                   >  1:1136943/1‑139 (MQ=255)

   gTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgat                                                                                                                                 <  1:1320078/139‑1 (MQ=255)

          cTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCt                                                                                                                          <  1:50512/139‑1 (MQ=255)

            ggCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTgg                                                                                                                        <  1:21393/139‑1 (MQ=255)

                  cAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTg                                                                                                                  <  1:985133/139‑1 (MQ=255)

                               aTTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               <  2:371510/113‑1 (MQ=255)

                               aTTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               >  1:371510/1‑113 (MQ=255)

                               aTTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATg                                                                                                     >  1:878786/1‑139 (MQ=255)

                                   aGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTa                                                                                                 <  2:1333156/139‑1 (MQ=255)

                                       ggtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgat                                                                                                                                 >  2:386224/1‑103 (MQ=255)

                                       ggtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgat                                                                                                                                 <  1:386224/103‑1 (MQ=255)

                                        gtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCt                                                                                                                          <  2:207022/109‑1 (MQ=255)

                                        gtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCt                                                                                                                          >  1:207022/1‑109 (MQ=255)

                                                 aTTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTcc                                                                                   <  2:1136943/139‑1 (MQ=255)

                                                     aCGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCt                                                                               >  2:1117904/1‑139 (MQ=255)

                                                          gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                <  2:159508/101‑1 (MQ=255)

                                                          gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                >  1:159508/1‑101 (MQ=255)

                                                          gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTa                                                                            <  2:1337105/137‑1 (MQ=255)

                                                          gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTa                                                                            >  1:1337105/1‑137 (MQ=255)

                                                                               tttGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCaa                                                     <  1:144161/139‑1 (MQ=255)

                                                                                ttGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAAt                                                    >  2:1189508/1‑139 (MQ=255)

                                                                                   tCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTa                                                                                                 >  2:902926/1‑91 (MQ=255)

                                                                                   tCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTa                                                                                                 <  1:902926/91‑1 (MQ=255)

                                                                                             cAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCgg                                       >  1:1226591/1‑139 (MQ=255)

                                                                                             cAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCgg                                       >  1:186108/1‑139 (MQ=255)

                                                                                                  tGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGc                                                                                           <  2:453814/82‑1 (MQ=255)

                                                                                                  tGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGc                                                                                           >  1:453814/1‑82 (MQ=255)

                                                                                                  tGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATtgt                                  >  2:590128/1‑139 (MQ=255)

                                                                                                    cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               >  1:260154/1‑44 (MQ=255)

                                                                                                    cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               <  2:260154/44‑1 (MQ=255)

                                                                                                    cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           >  2:1351632/1‑112 (MQ=255)

                                                                                                    cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           <  1:1351632/112‑1 (MQ=255)

                                                                                                                      tactCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATc              >  1:815924/1‑139 (MQ=255)

                                                                                                                        ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                <  1:168230/39‑1 (MQ=255)

                                                                                                                        ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                >  2:168230/1‑39 (MQ=255)

                                                                                                                        ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           >  1:114993/1‑92 (MQ=255)

                                                                                                                        ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           <  2:114993/92‑1 (MQ=255)

                                                                                                                        ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAg            >  1:1205577/1‑139 (MQ=255)

                                                                                                                          cccTCAACCGGGGCAGTGATGGGAGCTGGTATCTGCGCTGTGAAAATGCTTATCGTCCAGAAGTCCCCCTGTATGCTTTCATGCTGACACAGGCAGTGGACTATGACCAGATCGTAGCAGGCTCCCGCAACCATCataa          >  2:951428/1‑136 (MQ=255)

                                                                                                                          cccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          <  2:187416/139‑1 (MQ=255)

                                                                                                                          cccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          >  2:1348660/1‑139 (MQ=255)

                                                                                                                          cccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          >  2:876512/1‑139 (MQ=255)

                                                                                                                           ccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGTTCCCGCAGCCATCAGAcc         <  2:815924/139‑1 (MQ=255)

                                                                                                                             tCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCgg       >  2:360315/1‑139 (MQ=255)

                                                                                                                              cAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAg            <  2:509191/133‑1 (MQ=255)

                                                                                                                              cAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAg            >  1:509191/1‑133 (MQ=255)

                                                                                                                              cAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGgt      >  2:1177077/1‑139 (MQ=255)

                                                                                                                                  cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          <  2:823195/131‑1 (MQ=255)

                                                                                                                                  cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          >  1:823195/1‑131 (MQ=255)

                                                                                                                                  cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTaa  <  2:1226591/139‑1 (MQ=255)

                                                                                                                                  cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTaa  <  1:1177077/139‑1 (MQ=255)

TGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAA  >  NC_000913/2073482‑2073750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A