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
A8 F1 I2 R1	765	53.2	2691310	93.4%	2513683	103.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,641,403	A→G	V51A (GTT→GCT)	cspB ←	Qin prophage, cold shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,641,403	0	A	G	100.0%	223.4 / NA	62	V51A (GTT→GCT)	cspB	Qin prophage, cold shock protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (35/27); total (35/27)

TCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAACCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCA  >  NC_000913/1641279‑1641537

tCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCa                                                                                                                          >  2:447459/1‑139 (MQ=255)

     aTCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCtttt                                                                                                                                  >  1:1284201/1‑126 (MQ=255)

     aTCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCtttt                                                                                                                                  <  2:1284201/126‑1 (MQ=255)

       ctctACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAgg                                                                                                                   <  1:319823/139‑1 (MQ=255)

             tCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGAt                                                                                                             <  1:447459/139‑1 (MQ=255)

               aGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATaa                                                                                                           >  2:233177/1‑139 (MQ=255)

                 gCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAAtt                                                                                                         >  1:1148829/1‑139 (MQ=255)

                 gCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAAtt                                                                                                         >  2:253129/1‑139 (MQ=255)

                                       tataCAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGaaaaa                                                                                   >  2:816059/1‑139 (MQ=255)

                                              aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCaaa                                                                                                                        <  2:931498/95‑1 (MQ=255)

                                              aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCaaa                                                                                                                        >  1:931498/1‑95 (MQ=255)

                                              aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGcaca                                                                             <  2:378712/138‑1 (MQ=255)

                                              aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGcaca                                                                             >  1:378712/1‑138 (MQ=255)

                                              aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaa                                                                            >  1:991280/1‑139 (MQ=255)

                                              aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaa                                                                            >  1:45816/1‑139 (MQ=255)

                                              aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaa                                                                            >  1:657835/1‑139 (MQ=255)

                                               cGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaaa                                                                           <  2:991280/139‑1 (MQ=255)

                                                 aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATa                                                                                                                      >  2:1268163/1‑94 (MQ=255)

                                                 aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATa                                                                                                                      <  1:1268163/94‑1 (MQ=255)

                                                 aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGca                                                                               <  1:194453/133‑1 (MQ=255)

                                                 aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGca                                                                               >  2:194453/1‑133 (MQ=255)

                                                 aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAaca                                                                         <  1:816059/139‑1 (MQ=255)

                                                  gCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                        <  2:1148829/139‑1 (MQ=255)

                                                                  aGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGca                                                                               >  2:570731/1‑116 (MQ=255)

                                                                  aGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGca                                                                               <  1:570731/116‑1 (MQ=255)

                                                                            aCATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAac                                                                          >  1:655951/1‑111 (MQ=255)

                                                                            aCATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAac                                                                          <  2:655951/111‑1 (MQ=255)

                                                                              aTTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATa                                            >  2:266424/1‑139 (MQ=255)

                                                                              aTTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATa                                            >  2:367048/1‑139 (MQ=255)

                                                                                  gctgctgcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGc                                        >  2:1103504/1‑139 (MQ=255)

                                                                                    tgctgcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                      <  1:945023/139‑1 (MQ=255)

                                                                                    tgctgcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                      <  1:266424/139‑1 (MQ=255)

                                                                                                      accacTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTa                    <  1:367048/139‑1 (MQ=255)

                                                                                                         acTCTCTATAGAGAAGGTAGCCTTTTGATCTTCAAATa                                                                                                                      >  1:833581/1‑38 (MQ=255)

                                                                                                         acTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATa                                                                                                                      <  2:833581/38‑1 (MQ=255)

                                                                                                         acTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAAc                 >  1:579491/1‑139 (MQ=255)

                                                                                                          ctctctATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                      >  1:484118/1‑117 (MQ=255)

                                                                                                          ctctctATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                      <  2:484118/117‑1 (MQ=255)

                                                                                                          ctctctATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAAcc                >  2:414449/1‑139 (MQ=255)

                                                                                                            ctctATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAATCCAt              <  2:657835/139‑1 (MQ=255)

                                                                                                                    agaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTaa      >  1:946688/1‑139 (MQ=255)

                                                                                                                    agaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTaa      >  2:258546/1‑139 (MQ=255)

                                                                                                                     gaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGaa                                                                                              >  2:729561/1‑50 (MQ=255)

                                                                                                                     gaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGaa                                                                                              <  1:729561/50‑1 (MQ=255)

                                                                                                                     gaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGca                                                                               >  1:297327/1‑65 (MQ=255)

                                                                                                                     gaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGca                                                                               <  2:297327/65‑1 (MQ=255)

                                                                                                                      aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATc                                                         >  2:860813/1‑86 (MQ=255)

                                                                                                                      aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATc                                                         <  1:860813/86‑1 (MQ=255)

                                                                                                                      aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAc    >  1:1258406/1‑139 (MQ=255)

                                                                                                                      aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAc    <  1:233177/139‑1 (MQ=255)

                                                                                                                       aGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaaa                                                                           >  2:267810/1‑67 (MQ=255)

                                                                                                                       aGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaaa                                                                           <  1:267810/67‑1 (MQ=255)

                                                                                                                       aGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACGGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAcc   >  1:852737/1‑139 (MQ=255)

                                                                                                                       aGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAcc   >  2:483264/1‑139 (MQ=255)

                                                                                                                       aGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAcc   >  2:1335092/1‑139 (MQ=255)

                                                                                                                        ggTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCa  >  1:233082/1‑139 (MQ=255)

                                                                                                                         gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTg                                                                                                <  2:276754/44‑1 (MQ=255)

                                                                                                                         gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGaaa                                                                                     >  1:233762/1‑55 (MQ=255)

                                                                                                                         gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                        <  2:741398/68‑1 (MQ=255)

                                                                                                                         gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                        <  2:790341/68‑1 (MQ=255)

                                                                                                                         gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                        >  1:741398/1‑68 (MQ=255)

                                                                                                                         gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTta                                                                 <  1:919935/75‑1 (MQ=255)

TCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAACCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACCA  >  NC_000913/1641279‑1641537

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