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
A6 F1 I1 R1	750	51.0	2595496	93.6%	2429384	106.4

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%	71.3 / NA	23	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 (12/11); total (12/11)

TCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAT  >  NC_000913/1381656‑1381919

tCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                >  2:506048/1‑138 (MQ=255)

tCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                <  1:506048/138‑1 (MQ=255)

  gTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCg                                                                                                                             <  1:413168/139‑1 (MQ=255)

            tACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCg                                                                                                                   >  1:1058120/1‑139 (MQ=255)

             aCGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGt                                                                                                                  <  2:255964/139‑1 (MQ=255)

             aCGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGt                                                                                                                  >  1:694953/1‑139 (MQ=255)

                          atTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCa                                                                                                     >  1:621550/1‑139 (MQ=255)

                           ttCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTcctgtctcttatac                                                                                                                  >  2:892623/1‑113 (MQ=255)

                           ttCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTcctgtctcttatac                                                                                                                  <  1:892623/125‑13 (MQ=255)

                            tCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATg                                                                                                   <  2:621550/139‑1 (MQ=255)

                              aTCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGTGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                <  2:919972/108‑1 (MQ=255)

                              aTCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                >  1:919972/1‑108 (MQ=255)

                                                                  aaaTTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGaaa                                                             >  2:1034846/1‑139 (MQ=255)

                                                                            ggCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTg                                                                                                                        <  1:590542/70‑1 (MQ=255)

                                                                            ggCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTg                                                                                                                        >  2:590542/1‑70 (MQ=255)

                                                                                       ccGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGaa                                        >  1:600923/1‑139 (MQ=255)

                                                                                                          ctACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCt                     <  2:1058120/139‑1 (MQ=255)

                                                                                                           tACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTAt                                                                                                       <  2:1055280/56‑1 (MQ=255)

                                                                                                           tACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTAt                                                                                                       >  1:1055280/1‑56 (MQ=255)

                                                                                                                     ttGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAgggg          >  1:310826/1‑139 (MQ=255)

                                                                                                                             aCGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAt  >  1:365129/1‑139 (MQ=255)

                                                                                                                             aCGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAt  <  2:600923/139‑1 (MQ=255)

                                                                                                                             aCGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAt  <  1:1034846/139‑1 (MQ=255)

TCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAT  >  NC_000913/1381656‑1381919

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `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