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 F28 I1 R1	134	60.5	2175152	94.0%	2044642	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,473,862	T→C	Y87H (TAT→CAT)	yfdP →	CPS‑53 (KpLE1) prophage; protein YfdP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,473,862	0	T	C	98.0%	176.5 / ‑5.8	50	Y87H (TAT→CAT)	yfdP	CPS‑53 (KpLE1) prophage; protein YfdP
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (21/28); minor base A (1/0); total (22/28)
Fisher's exact test for biased strand distribution p-value = 4.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAGGTAAGGTCTCACTCAACCTGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGTATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCTTAATTAACTAATTATTTATCTCA  >  NC_000913/2473727‑2473998

aaaGGTAAGGTCTCACTCAACCTGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGatgcat                                                                                                                                        >  2:406377/1‑138 (MQ=255)

      aaggtCTCACTCAACCTGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATcg                                                                                                                                <  2:909223/140‑1 (MQ=255)

             cactcaACCTGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCggtggt                                                                                                                         <  1:678635/140‑1 (MQ=255)

             cactcaACCTGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCggtggt                                                                                                                         <  1:319208/140‑1 (MQ=255)

               ctcaACCTGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCg                                                                                                                       <  1:574692/140‑1 (MQ=255)

                      tGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACt                                                                                                                <  2:608287/140‑1 (MQ=255)

                               aaCCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCggtggt                                                                                                                         <  1:145621/122‑1 (MQ=255)

                               aaCCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCggtggt                                                                                                                         >  2:145621/1‑122 (MQ=255)

                               aaCCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAg                                                                                                       >  2:915685/1‑140 (MQ=255)

                                aCCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAgg                                                                                                      <  2:535630/140‑1 (MQ=255)

                                aCCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAgg                                                                                                      <  1:915685/140‑1 (MQ=255)

                                aCCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAgg                                                                                                      <  1:1078356/140‑1 (MQ=255)

                                aCCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAgg                                                                                                      <  1:1057113/140‑1 (MQ=255)

                                      tgatgaGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGAcc                                                                                                >  1:943761/1‑140 (MQ=255)

                                            gaACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGAc                                                                                          >  1:14556/1‑140 (MQ=255)

                                              aCCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGa                                                                                                     >  2:98162/1‑127 (MQ=255)

                                              aCCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGa                                                                                                     <  1:98162/127‑1 (MQ=255)

                                               ccGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAAt                                                                                       >  1:1030209/1‑140 (MQ=255)

                                                  tCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTTAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTAc                                                                                    >  1:588295/1‑140 (MQ=255)

                                                  tCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTAc                                                                                    >  2:822756/1‑140 (MQ=255)

                                                  tCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTAc                                                                                    >  2:774549/1‑140 (MQ=255)

                                                      aaaaTCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGAc                                                                                <  1:774549/140‑1 (MQ=255)

                                                          tCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCtt                                                                            >  1:817428/1‑140 (MQ=255)

                                                              acacAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGAc                                                                                <  1:106325/132‑1 (MQ=255)

                                                              acacAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGAc                                                                                >  2:106325/1‑132 (MQ=255)

                                                                acaAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGAATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGt                                                                      >  2:755666/1‑140 (MQ=255)

                                                                  aaaCTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGa                                                                    >  2:892531/1‑140 (MQ=255)

                                                                    aCTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGc                                                                  >  2:883964/1‑140 (MQ=255)

                                                                    aCTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGc                                                                  >  2:575209/1‑140 (MQ=255)

                                                                     ctctCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGcc                                                                 >  1:182842/1‑140 (MQ=255)

                                                                       ctcATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTTAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTg                                                               <  2:588295/140‑1 (MQ=255)

                                                                       ctcATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTg                                                               <  2:766663/140‑1 (MQ=255)

                                                                                  gCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTc                                                    >  2:875728/1‑140 (MQ=255)

                                                                                  gCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTc                                                    >  1:32820/1‑140 (MQ=255)

                                                                                    ccGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCcg                                                  <  2:32820/140‑1 (MQ=255)

                                                                                       aCTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTg                                                               >  1:780453/1‑124 (MQ=255)

                                                                                       aCTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTg                                                               <  2:780453/124‑1 (MQ=255)

                                                                                       aCTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCcg                                                  >  1:130729/1‑137 (MQ=255)

                                                                                       aCTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCcg                                                  <  2:130729/137‑1 (MQ=255)

                                                                                            ccGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGcagcag                                          <  1:892531/140‑1 (MQ=255)

                                                                                            ccGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGcagcag                                          <  1:875728/140‑1 (MQ=255)

                                                                                            ccGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGcagcag                                          <  2:943761/140‑1 (MQ=255)

                                                                                                 ggAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCAt                                     <  2:908064/140‑1 (MQ=255)

                                                                                                  gAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGcagcag                                          >  2:188955/1‑134 (MQ=255)

                                                                                                  gAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGcagcag                                          <  1:188955/134‑1 (MQ=255)

                                                                                                                   acacCACCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCttaatta                   <  1:532702/140‑1 (MQ=255)

                                                                                                                    caccacCGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCttaattaa                  <  2:798221/140‑1 (MQ=255)

                                                                                                                      ccaccGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCTTAATTAACt                <  2:817428/140‑1 (MQ=255)

                                                                                                                      ccaccGAAACGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCTTAATTAACt                <  2:862294/140‑1 (MQ=255)

                                                                                                                               cGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCtta                       <  2:221082/124‑1 (MQ=255)

                                                                                                                               cGCCGATGCATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCtta                       >  1:221082/1‑124 (MQ=255)

                                                                                                                                    atgcatgtCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCTTAATTAACt                <  1:994302/126‑1 (MQ=255)

                                                                                                                                    atgcatgtCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCTTAATTAACTAATTATTTATCtca  <  1:653200/140‑1 (MQ=255)

AAAGGTAAGGTCTCACTCAACCTGGAAATCGAACCATTTGATGAGAACCGTCTGAAAATCAAACACAAACTCTCATATGTTCGCCCGACTAACCGTGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGTATGTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAGCCTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCATTCTTAATTAACTAATTATTTATCTCA  >  NC_000913/2473727‑2473998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A