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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,381,789	G→A	pseudogene (13/126 nt)	ycjV →	pseudogene, putative ATP‑binding component of a transport system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,381,789	0	G	A	100.0%	94.4 / NA	30	pseudogene (13/126 nt)	ycjV	pseudogene, putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (15/15); total (15/15)

TCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCATTCCC  >  NC_000913/1381656‑1381923

tCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTc                                                                                                                                   >  2:226164/1‑139 (MQ=255)

tCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTc                                                                                                                                   >  2:76698/1‑139 (MQ=255)

   tGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGt                                                                                                                                >  2:733554/1‑139 (MQ=255)

         gAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGt                                                                                                                          <  1:226164/139‑1 (MQ=255)

         gAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGt                                                                                                                          <  1:76698/139‑1 (MQ=255)

                           ttCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCAt                                                                                                        >  1:249268/1‑139 (MQ=255)

                            tCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATg                                                                                                       <  1:733554/139‑1 (MQ=255)

                               tCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAg                                                                                                    >  1:789576/1‑139 (MQ=255)

                                     cgcgCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                    <  2:282091/101‑1 (MQ=255)

                                     cgcgCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                    >  1:282091/1‑101 (MQ=255)

                                          aaGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATc                                                                                         <  2:586473/139‑1 (MQ=255)

                                                                        gCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCAt                                                           <  2:249268/139‑1 (MQ=255)

                                                                        gCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCAt                                                           <  1:690367/139‑1 (MQ=255)

                                                                                           tGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACgg                                        >  2:768968/1‑139 (MQ=255)

                                                                                                     aTGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAAt                              >  1:661802/1‑139 (MQ=255)

                                                                                                           tACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTa                        >  1:151040/1‑139 (MQ=255)

                                                                                                             caccacGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTaaa                      <  2:151040/139‑1 (MQ=255)

                                                                                                                   ggTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCa                                                                                        >  1:576796/1‑67 (MQ=255)

                                                                                                                   ggTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCa                                                                                        <  2:576796/67‑1 (MQ=255)

                                                                                                                     ttGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTCGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAgggg              >  2:504125/1‑139 (MQ=255)

                                                                                                                       gggggCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGa            <  1:726827/139‑1 (MQ=255)

                                                                                                                       gggggCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGa            >  2:389885/1‑139 (MQ=255)

                                                                                                                          ggCACAAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGga                                                                                                  <  2:171473/50‑1 (MQ=255)

                                                                                                                          ggCACAAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGga                                                                                                  >  1:171473/1‑50 (MQ=255)

                                                                                                                           gCACTAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGc        <  1:768968/139‑1 (MQ=255)

                                                                                                                             aCGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAt      >  1:13859/1‑139 (MQ=255)

                                                                                                                             aCGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAt      <  2:789576/139‑1 (MQ=255)

                                                                                                                              cGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAata                                                                                           >  2:181041/1‑53 (MQ=255)

                                                                                                                              cGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAata                                                                                           <  1:181041/53‑1 (MQ=255)

                                                                                                                                 gTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCATTccc  <  2:13859/139‑1 (MQ=255)

TCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCATTCCC  >  NC_000913/1381656‑1381923

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