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 I2 R1 760 67.6 3323148 92.7% 3080558 109.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,146,011 C→T *195* (TAG→TAA)  yceF ← m(7)GTP pyrophosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,146,0110CT98.1% 167.1 / ‑5.5 53*195* (TAG→TAA) yceFm(7)GTP pyrophosphatase
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (29/23);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 4.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGCGTAACGCGCGCTAATACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAACTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCACTCT  >  NC_000913/1145882‑1146141
                                                                                                                                 |                                                                                                                                  
cTGCGTAACGCGCGCTAATACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATc                                                                                                                           >  1:8536/1‑139 (MQ=255)
                       gCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                    >  2:421019/1‑139 (MQ=255)
                       gCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                    <  1:977108/139‑1 (MQ=255)
                         atatAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                  >  2:1469080/1‑139 (MQ=255)
                         atatAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                  <  1:1469080/139‑1 (MQ=255)
                           ataAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAAc                                                                                                >  1:1193440/1‑139 (MQ=255)
                           ataAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAAc                                                                                                >  1:1393636/1‑139 (MQ=255)
                           ataAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAAc                                                                                                >  1:1510824/1‑139 (MQ=255)
                           ataAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACATAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCAGACGTAAc                                                                                                >  2:1005001/1‑139 (MQ=255)
                                   gATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGaca                                                                                        <  2:1595209/139‑1 (MQ=255)
                                   gATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGaca                                                                                        <  2:1393636/139‑1 (MQ=255)
                                        tGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAgcg                                                                                   >  1:209281/1‑139 (MQ=255)
                                        tGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATAATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAgcg                                                                                   >  2:1635046/1‑139 (MQ=255)
                                           gCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                  >  2:946427/1‑121 (MQ=255)
                                           gCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                  <  1:946427/121‑1 (MQ=255)
                                            cGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGAt                                                                               <  2:435811/139‑1 (MQ=255)
                                              gTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttccc                                                                                                        >  1:1176173/1‑112 (MQ=255)
                                              gTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttccc                                                                                                        <  2:1176173/112‑1 (MQ=255)
                                              gTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTa                                                                             >  2:647090/1‑139 (MQ=255)
                                                 ggCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTGTCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCg                                                                          >  1:104583/1‑139 (MQ=255)
                                                  gCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCgg                                                                         >  1:1549961/1‑139 (MQ=255)
                                                     tGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTaa                                                                      <  2:1510824/139‑1 (MQ=255)
                                                         aaGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAaacca                                                                  >  2:683282/1‑139 (MQ=255)
                                                            gCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAaaccaacc                                                               >  1:213296/1‑139 (MQ=255)
                                                            gCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAaaccaacc                                                               <  2:1549961/139‑1 (MQ=255)
                                                             cGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAaccaacca                                                              <  1:1309656/139‑1 (MQ=255)
                                                              gTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAg                                                             <  2:353485/139‑1 (MQ=255)
                                                                ttACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttcc                                                                                                         <  2:173437/93‑1 (MQ=255)
                                                                ttACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttcc                                                                                                         >  1:173437/1‑93 (MQ=255)
                                                                 tACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                  <  1:201314/99‑1 (MQ=255)
                                                                 tACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                  >  2:201314/1‑99 (MQ=255)
                                                                      cgcATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAg                                                                                                                         <  1:256352/71‑1 (MQ=255)
                                                                      cgcATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAg                                                                                                                         >  2:256352/1‑71 (MQ=255)
                                                                        cATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAaaccaac                                                                >  2:363144/1‑126 (MQ=255)
                                                                        cATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAaaccaac                                                                <  1:363144/126‑1 (MQ=255)
                                                                               ccggcAGCATCGATTGCCGGATGCGACGTAATCACTTACGGCACAAAAAACCATCCCATCAGCGGGTTTATCCCTTGCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATTACGcc                                            <  2:1374216/139‑1 (MQ=255)
                                                                                cgccAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGccc                                           >  2:699265/1‑139 (MQ=255)
                                                                                     gCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTa                                      <  2:209281/139‑1 (MQ=255)
                                                                                                      cGAGGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGt                                                                                                                    <  1:1009837/44‑1 (MQ=255)
                                                                                                      cGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGt                                                                                                                    >  2:1009837/1‑44 (MQ=255)
                                                                                                             aCCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCaa              >  2:1477738/1‑139 (MQ=255)
                                                                                                                 caTGCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGAt                                                                               >  1:1126983/1‑70 (MQ=255)
                                                                                                                 caTCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGAt                                                                               <  2:1126983/70‑1 (MQ=255)
                                                                                                                   tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                    <  2:1022013/47‑1 (MQ=255)
                                                                                                                   tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                    >  1:1022013/1‑47 (MQ=255)
                                                                                                                   tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCtt        >  2:620289/1‑139 (MQ=255)
                                                                                                                    ccGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTc       <  1:421019/139‑1 (MQ=255)
                                                                                                                        cgcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAg                                                             <  2:1502408/81‑1 (MQ=255)
                                                                                                                        cgcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAg                                                             >  1:1502408/1‑81 (MQ=255)
                                                                                                                        cgcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCActc   >  2:46120/1‑139 (MQ=255)
                                                                                                                         gcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCActct  <  1:699265/139‑1 (MQ=255)
                                                                                                                         gcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACACTCAAACAGCGTAATGCCAAATCCTTc       <  2:1456022/134‑1 (MQ=255)
                                                                                                                         gcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACACTCAAACAGCGTAATGCCAAATCCTTc       >  1:1456022/1‑134 (MQ=255)
                                                                                                                                 |                                                                                                                                  
CTGCGTAACGCGCGCTAATACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAACTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCACTCT  >  NC_000913/1145882‑1146141

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